Starting phenix.real_space_refine
on Fri Jul  3 05:39:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zjr_60154/07_2026/8zjr_60154.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zjr_60154/07_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_60154/07_2026/8zjr_60154.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zjr_60154/07_2026/8zjr_60154.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zjr_60154/07_2026/8zjr_60154.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zjr_60154/07_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-dev-6108/lib/python3.11/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: 3.70, per 1000 atoms: 0.30
  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: 1.04
  Conformation dependent library (CDL) restraints added in 621.6 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: 1.51
  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: 2.01

  Time building geometry restraints manager: 1.39 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=" C3'  DC J  27 "
       pdb=" C2'  DC J  27 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.22e+01
  bond pdb=" C3'  DT I 114 "
       pdb=" C2'  DT I 114 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.12e+01
  bond pdb=" C1'  DT J 111 "
       pdb=" N1   DT J 111 "
    ideal  model  delta    sigma   weight residual
    1.468  1.511 -0.043 1.40e-02 5.10e+03 9.40e+00
  bond pdb=" C3'  DC I  15 "
       pdb=" C2'  DC I  15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.84e+00
  bond pdb=" C3'  DC I 137 "
       pdb=" C2'  DC I 137 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.32e+00
  ... (remaining 12970 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 17803
        1.76 -     3.53: 816
        3.53 -     5.29: 19
        5.29 -     7.05: 6
        7.05 -     8.81: 1
  Bond angle restraints: 18645
  Sorted by residual:
  angle pdb=" O4'  DG I  97 "
        pdb=" C4'  DG I  97 "
        pdb=" C3'  DG I  97 "
      ideal   model   delta    sigma   weight residual
     106.00  102.51    3.49 6.00e-01 2.78e+00 3.38e+01
  angle pdb=" O4'  DA J  99 "
        pdb=" C4'  DA J  99 "
        pdb=" C3'  DA J  99 "
      ideal   model   delta    sigma   weight residual
     106.00  103.02    2.98 6.00e-01 2.78e+00 2.47e+01
  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=" O4'  DA J 112 "
        pdb=" C4'  DA J 112 "
        pdb=" C3'  DA J 112 "
      ideal   model   delta    sigma   weight residual
     106.00  103.19    2.81 6.00e-01 2.78e+00 2.20e+01
  angle pdb=" O4'  DG I  46 "
        pdb=" C4'  DG I  46 "
        pdb=" C3'  DG I  46 "
      ideal   model   delta    sigma   weight residual
     106.00  103.19    2.81 6.00e-01 2.78e+00 2.19e+01
  ... (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 -    0.044: 1575
       0.044 -    0.089: 415
       0.089 -    0.133: 103
       0.133 -    0.178: 5
       0.178 -    0.222: 2
  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     -2.73   -2.51   -0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" C3'  DT I  57 "
            pdb=" C4'  DT I  57 "
            pdb=" O3'  DT I  57 "
            pdb=" C2'  DT I  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.55   -0.18 2.00e-01 2.50e+01 8.34e-01
  chirality pdb=" C3'  DC I  53 "
            pdb=" C4'  DC I  53 "
            pdb=" O3'  DC I  53 "
            pdb=" C2'  DC I  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.56   -0.17 2.00e-01 2.50e+01 7.08e-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:             2.150
  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:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.960
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.123  12975  Z= 0.474
  Angle     :  0.705   8.813  18645  Z= 0.641
  Chirality :  0.042   0.222   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/Z
  covalent geometry    : bond        0.00553 /  0.47 (12975)
  covalent geometry    : angle       0.70486 /  0.64 (18645)
  hydrogen bonds       : bond        0.10459 /  6.73 (  757)
  hydrogen bonds       : angle       3.81033 /  2.79 ( 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  : 0.260 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 79
  average time/residue: 0.1325
  time to fit residues: 14.2571
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  : 0.222 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 53 optimal weight:   10.0000
   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:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.4980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.4100 r_free = 0.4100 target = 0.180716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.125674 restraints weight = 78023.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 5.14
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3407
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3407 r_free = 0.3407    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3406 r_free = 0.3406    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (9 function evaluations)
r_final: 0.3406
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.0533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  12975  Z= 0.165
  Angle     :  0.596   7.201  18645  Z= 0.356
  Chirality :  0.044   0.333   2100
  Planarity :  0.004   0.044   1462
  Dihedral  : 30.458 178.477   3850
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 19.69 %
    Favored  : 79.05 %
  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:  1.29 (0.29), residues: 859
  helix:  1.77 (0.21), residues: 604
  sheet: -5.18 (0.65), residues: 14
  loop : -1.14 (0.36), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  36 
 TYR   0.010   0.001   TYR D  41 
 PHE   0.008   0.001   PHE E  68 
 TRP   0.001   0.000   TRP M  95 
 HIS   0.004   0.001   HIS F  76 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.17 (12975)
  covalent geometry    : angle       0.59577 /  0.36 (18645)
  hydrogen bonds       : bond        0.05267 /  3.59 (  757)
  hydrogen bonds       : angle       3.13165 /  2.24 ( 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
  83 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A   59 THR cc_start: 0.9303 (p) cc_final: 0.9097 (p)
REVERT: A   60 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7329 (pm20)
REVERT: E   60 GLU cc_start: 0.8457 (pm20) cc_final: 0.8102 (pm20)
  outliers start: 7
  outliers final: 5
  residues processed: 81
  average time/residue: 0.1346
  time to fit residues: 14.9182
Evaluate side-chains
  79 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain B residue   50 LEU
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 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:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 63 optimal weight:    5.9990
   chunk 78 optimal weight:    9.9990
   chunk 13 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.7180

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.181126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.126510 restraints weight = 79059.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 5.23
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3414
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3414 r_free = 0.3414    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3414 r_free = 0.3414    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (11 function evaluations)
r_final: 0.3414
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.0660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12975  Z= 0.153
  Angle     :  0.571   7.356  18645  Z= 0.342
  Chirality :  0.042   0.317   2100
  Planarity :  0.004   0.042   1462
  Dihedral  : 30.460 178.152   3849
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 19.83 %
    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:  1.41 (0.29), residues: 859
  helix:  1.90 (0.21), residues: 604
  sheet: -5.19 (0.64), residues: 14
  loop : -1.18 (0.36), 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   0.010   0.001   PHE E  68 
 TRP   0.001   0.000   TRP M  95 
 HIS   0.004   0.001   HIS F  76 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.15 (12975)
  covalent geometry    : angle       0.57081 /  0.34 (18645)
  hydrogen bonds       : bond        0.04869 /  3.32 (  757)
  hydrogen bonds       : angle       3.01812 /  2.15 ( 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
  86 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A   59 THR cc_start: 0.9272 (p) cc_final: 0.9047 (p)
REVERT: A   60 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7479 (pm20)
REVERT: C  100 ARG cc_start: 0.7603 (mtp85) cc_final: 0.7403 (mtp85)
  outliers start: 8
  outliers final: 4
  residues processed: 83
  average time/residue: 0.1261
  time to fit residues: 14.2702
Evaluate side-chains
  79 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
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   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:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 70 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 105 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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
M 103 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.178869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.122459 restraints weight = 76334.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 4.94
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3373
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3373 r_free = 0.3373    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3373 r_free = 0.3373    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3373
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.0925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  12975  Z= 0.237
  Angle     :  0.647   7.923  18645  Z= 0.370
  Chirality :  0.046   0.359   2100
  Planarity :  0.004   0.041   1462
  Dihedral  : 30.649 176.734   3849
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 20.81 %
    Favored  : 77.51 %
  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:  1.12 (0.29), residues: 859
  helix:  1.69 (0.21), residues: 604
  sheet: -5.27 (0.64), residues: 14
  loop : -1.31 (0.35), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG M 118 
 TYR   0.012   0.002   TYR B  52 
 PHE   0.014   0.002   PHE E  68 
 TRP   0.002   0.001   TRP M  95 
 HIS   0.003   0.001   HIS C  83 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00526 /  0.24 (12975)
  covalent geometry    : angle       0.64692 /  0.37 (18645)
  hydrogen bonds       : bond        0.05347 /  3.62 (  757)
  hydrogen bonds       : angle       3.09212 /  2.21 ( 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
  89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.200 
Fit side-chains
REVERT: C  100 ARG cc_start: 0.7695 (mtp85) cc_final: 0.7491 (mtp85)
  outliers start: 10
  outliers final: 8
  residues processed: 86
  average time/residue: 0.1172
  time to fit residues: 13.6894
Evaluate side-chains
  84 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain D residue   48 GLN
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 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:    0.5980
   chunk 64 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 49 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 79 optimal weight:   10.0000
   chunk 86 optimal weight:   20.0000
   chunk 72 optimal weight:   30.0000
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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
** 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**
** M 103 HIS ** 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 = 0.4093 r_free = 0.4093 target = 0.179828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.124068 restraints weight = 72119.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 4.84
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3389
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (8 function evaluations)
r_final: 0.3389
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.0923

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= 0.146
  Angle     :  0.578   7.651  18645  Z= 0.340
  Chirality :  0.043   0.323   2100
  Planarity :  0.004   0.039   1462
  Dihedral  : 30.549 178.778   3849
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 21.79 %
    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:  1.39 (0.29), residues: 859
  helix:  1.89 (0.21), residues: 604
  sheet: -5.24 (0.63), residues: 14
  loop : -1.23 (0.35), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG M 165 
 TYR   0.012   0.001   TYR D  41 
 PHE   0.011   0.001   PHE E  68 
 TRP   0.001   0.000   TRP M  95 
 HIS   0.008   0.001   HIS M 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.15 (12975)
  covalent geometry    : angle       0.57767 /  0.34 (18645)
  hydrogen bonds       : bond        0.04692 /  3.20 (  757)
  hydrogen bonds       : angle       2.96271 /  2.11 ( 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
  81 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.197 
Fit side-chains
REVERT: C  100 ARG cc_start: 0.7558 (mtp85) cc_final: 0.7330 (mtp85)
  outliers start: 5
  outliers final: 3
  residues processed: 80
  average time/residue: 0.1255
  time to fit residues: 13.5689
Evaluate side-chains
  78 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain E residue   83 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:    1.9990
   chunk 87 optimal weight:   20.0000
   chunk 98 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 10 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9990
   chunk 86 optimal weight:   20.0000
   chunk 21 optimal weight:    0.6980
   chunk 83 optimal weight:   10.0000
   chunk 103 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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
** D  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  26 ASN
** M 103 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 = 0.4097 r_free = 0.4097 target = 0.180134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.123667 restraints weight = 63615.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 4.13
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3385
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3385 r_free = 0.3385    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3385 r_free = 0.3385    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3385
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.1016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12975  Z= 0.153
  Angle     :  0.573   7.568  18645  Z= 0.336
  Chirality :  0.042   0.320   2100
  Planarity :  0.004   0.040   1462
  Dihedral  : 30.497 178.592   3849
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 21.65 %
    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:  1.48 (0.29), residues: 859
  helix:  1.97 (0.21), residues: 604
  sheet: -5.23 (0.64), residues: 14
  loop : -1.22 (0.35), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG M 165 
 TYR   0.012   0.001   TYR D  41 
 PHE   0.011   0.001   PHE E  68 
 TRP   0.001   0.001   TRP M  95 
 HIS   0.006   0.001   HIS M 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.15 (12975)
  covalent geometry    : angle       0.57278 /  0.34 (18645)
  hydrogen bonds       : bond        0.04599 /  3.14 (  757)
  hydrogen bonds       : angle       2.91179 /  2.08 ( 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
  86 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.291 
Fit side-chains
REVERT: C  100 ARG cc_start: 0.7502 (mtp85) cc_final: 0.7262 (mtp85)
REVERT: D   94 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7130 (mp0)
REVERT: E   60 GLU cc_start: 0.8357 (pm20) cc_final: 0.8138 (pm20)
  outliers start: 10
  outliers final: 8
  residues processed: 84
  average time/residue: 0.1129
  time to fit residues: 13.0111
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  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue   94 GLU
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 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:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 79 optimal weight:   10.0000
   chunk 28 optimal weight:    0.8980
   chunk 78 optimal weight:   10.0000
   chunk 41 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 98 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 73 optimal weight:    9.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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
** 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**
** M 103 HIS ** 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 = 0.4097 r_free = 0.4097 target = 0.180133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.124880 restraints weight = 75125.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 5.01
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3394
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3394
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1053

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= 0.154
  Angle     :  0.574   7.596  18645  Z= 0.336
  Chirality :  0.042   0.324   2100
  Planarity :  0.004   0.040   1462
  Dihedral  : 30.480 178.461   3849
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 20.95 %
    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:  1.52 (0.29), residues: 859
  helix:  2.01 (0.21), residues: 604
  sheet: -5.25 (0.62), residues: 14
  loop : -1.21 (0.35), residues: 241

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   0.011   0.001   PHE E  68 
 TRP   0.001   0.000   TRP M  95 
 HIS   0.005   0.001   HIS M 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.15 (12975)
  covalent geometry    : angle       0.57375 /  0.34 (18645)
  hydrogen bonds       : bond        0.04567 /  3.12 (  757)
  hydrogen bonds       : angle       2.89791 /  2.07 ( 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
  89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.270 
Fit side-chains
REVERT: C  100 ARG cc_start: 0.7564 (mtp85) cc_final: 0.7313 (mtp85)
REVERT: D   94 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7003 (mp0)
REVERT: E   60 GLU cc_start: 0.8334 (pm20) cc_final: 0.8073 (pm20)
  outliers start: 11
  outliers final: 10
  residues processed: 88
  average time/residue: 0.1125
  time to fit residues: 13.5985
Evaluate side-chains
  87 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain D residue   91 THR
Chi-restraints excluded: chain D residue   94 GLU
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain E residue   83 LEU
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain G residue   20 SER
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:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 92 optimal weight:    9.9990
   chunk 102 optimal weight:    2.9990
   chunk 74 optimal weight:   20.0000
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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
D  64 ASN
** D  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  26 ASN
** M 103 HIS ** 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 = 0.4111 r_free = 0.4111 target = 0.180756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.126560 restraints weight = 75393.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 5.03
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3404
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3404 r_free = 0.3404    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3404 r_free = 0.3404    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.3404
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.1200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12975  Z= 0.177
  Angle     :  0.597   7.770  18645  Z= 0.344
  Chirality :  0.043   0.338   2100
  Planarity :  0.004   0.040   1462
  Dihedral  : 30.511 177.081   3849
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 20.95 %
    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:  1.45 (0.29), residues: 859
  helix:  1.95 (0.21), residues: 605
  sheet: -5.27 (0.63), residues: 14
  loop : -1.24 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M 165 
 TYR   0.010   0.001   TYR G  58 
 PHE   0.014   0.001   PHE E  68 
 TRP   0.002   0.001   TRP M  95 
 HIS   0.004   0.001   HIS M 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.18 (12975)
  covalent geometry    : angle       0.59676 /  0.34 (18645)
  hydrogen bonds       : bond        0.04769 /  3.24 (  757)
  hydrogen bonds       : angle       2.94421 /  2.10 ( 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
  94 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.266 
Fit side-chains
REVERT: C  100 ARG cc_start: 0.7604 (mtp85) cc_final: 0.7338 (mtp85)
REVERT: E   60 GLU cc_start: 0.8299 (pm20) cc_final: 0.8027 (pm20)
  outliers start: 15
  outliers final: 12
  residues processed: 91
  average time/residue: 0.1181
  time to fit residues: 14.5383
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  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain D residue   91 THR
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   51 ILE
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain G residue   20 SER
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:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 86 optimal weight:   20.0000
   chunk 84 optimal weight:   10.0000
   chunk 48 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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
M 103 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.181922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.125737 restraints weight = 68656.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 4.62
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3415
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3415 r_free = 0.3415    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3415 r_free = 0.3415    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (8 function evaluations)
r_final: 0.3415
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1216

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= 0.152
  Angle     :  0.574   8.143  18645  Z= 0.334
  Chirality :  0.042   0.338   2100
  Planarity :  0.004   0.040   1462
  Dihedral  : 30.459 178.264   3849
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 21.23 %
    Favored  : 76.54 %
  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:  1.58 (0.29), residues: 859
  helix:  2.05 (0.21), residues: 605
  sheet: -5.28 (0.63), residues: 14
  loop : -1.21 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  46 
 TYR   0.011   0.001   TYR D  41 
 PHE   0.012   0.001   PHE E  68 
 TRP   0.002   0.001   TRP M  95 
 HIS   0.005   0.001   HIS M 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.15 (12975)
  covalent geometry    : angle       0.57436 /  0.33 (18645)
  hydrogen bonds       : bond        0.04523 /  3.09 (  757)
  hydrogen bonds       : angle       2.89403 /  2.07 ( 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
  90 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7261 (pm20)
REVERT: C  100 ARG cc_start: 0.7572 (mtp85) cc_final: 0.7307 (mtp85)
REVERT: E   60 GLU cc_start: 0.8311 (pm20) cc_final: 0.8081 (pm20)
  outliers start: 14
  outliers final: 12
  residues processed: 87
  average time/residue: 0.1126
  time to fit residues: 13.4918
Evaluate side-chains
  89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
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   31 THR
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain D residue   91 THR
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   51 ILE
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain G residue   20 SER
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 90 optimal weight:   10.0000
   chunk 101 optimal weight:    0.6980
   chunk 94 optimal weight:   10.0000
   chunk 16 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0770
   chunk 75 optimal weight:   10.0000
   chunk 96 optimal weight:   10.0000
   overall best weight:    0.6738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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
M  98 ASN
M 103 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.182396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.126032 restraints weight = 62827.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 4.02
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3425
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3425 r_free = 0.3425    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3425 r_free = 0.3425    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3425
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.1226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12975  Z= 0.148
  Angle     :  0.574   8.658  18645  Z= 0.335
  Chirality :  0.042   0.337   2100
  Planarity :  0.004   0.045   1462
  Dihedral  : 30.450 178.204   3849
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 20.95 %
    Favored  : 76.54 %
  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:  1.62 (0.29), residues: 859
  helix:  2.08 (0.21), residues: 605
  sheet: -5.26 (0.63), residues: 14
  loop : -1.19 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG F  24 
 TYR   0.011   0.001   TYR D  41 
 PHE   0.011   0.001   PHE E  68 
 TRP   0.005   0.002   TRP M  95 
 HIS   0.005   0.001   HIS M 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.15 (12975)
  covalent geometry    : angle       0.57444 /  0.34 (18645)
  hydrogen bonds       : bond        0.04467 /  3.06 (  757)
  hydrogen bonds       : angle       2.88160 /  2.06 ( 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
  93 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7320 (pm20)
REVERT: C  100 ARG cc_start: 0.7501 (mtp85) cc_final: 0.7244 (mtp85)
REVERT: E   60 GLU cc_start: 0.8339 (pm20) cc_final: 0.8116 (pm20)
  outliers start: 16
  outliers final: 12
  residues processed: 88
  average time/residue: 0.1192
  time to fit residues: 14.6340
Evaluate side-chains
  89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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   91 THR
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   20 SER
Chi-restraints excluded: chain H residue   58 LYS
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain M residue   98 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 49 optimal weight:    0.6980
   chunk 76 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   chunk 73 optimal weight:   10.9990
   chunk 37 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   chunk 96 optimal weight:   10.0000
   chunk 19 optimal weight:    0.6980
   chunk 20 optimal weight:    0.3980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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
M 103 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.182785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.125864 restraints weight = 63853.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 4.05
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3423
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3423
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
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   0.041  12975  Z= 0.143
  Angle     :  0.564   8.594  18645  Z= 0.329
  Chirality :  0.042   0.337   2100
  Planarity :  0.004   0.039   1462
  Dihedral  : 30.440 178.163   3849
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 21.09 %
    Favored  : 76.54 %
  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:  2.10 (0.21), residues: 606
  sheet: -5.25 (0.63), residues: 14
  loop : -1.15 (0.36), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG M  97 
 TYR   0.011   0.001   TYR D  41 
 PHE   0.011   0.001   PHE E  68 
 TRP   0.006   0.002   TRP M  95 
 HIS   0.008   0.001   HIS M  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.14 (12975)
  covalent geometry    : angle       0.56380 /  0.33 (18645)
  hydrogen bonds       : bond        0.04461 /  3.05 (  757)
  hydrogen bonds       : angle       2.87868 /  2.05 ( 1928)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1940.38 seconds
wall clock time: 34 minutes 4.55 seconds (2044.55 seconds total)