Starting phenix.real_space_refine
on Thu May 15 21:52:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yi1_33848/05_2025/7yi1_33848.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yi1_33848/05_2025/7yi1_33848.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yi1_33848/05_2025/7yi1_33848.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yi1_33848/05_2025/7yi1_33848.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yi1_33848/05_2025/7yi1_33848.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yi1_33848/05_2025/7yi1_33848.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     302      5.49       5
     S      21      5.16       5
     C    7843      2.51       5
     N    2576      2.21       5
     O    3184      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13926
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "B"
      Number of atoms: 633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 633
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 823
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "F"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 646
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "G"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 823
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 3076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 3076
          Classifications: {'DNA': 151}
          Link IDs: {'rna3p': 150}
    Chain: "J"
      Number of atoms: 3115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 3115
          Classifications: {'DNA': 151}
          Link IDs: {'rna3p': 150}
    Chain: "K"
      Number of atoms: 853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 853
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 853
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 830
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'M3L:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "E"
      Number of atoms: 822
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 822
          Classifications: {'peptide': 99}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'M3L:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 8.27, per 1000 atoms: 0.59
  Number of scatterers: 13926
  At special positions: 0
  Unit cell: (139.643, 141.808, 106.085, 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      21     16.00
     P     302     15.00
     O    3184      8.00
     N    2576      7.00
     C    7843      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.28
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1812

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 14 sheets defined
      63.0% alpha, 11.6% beta
      146 base pairs and 259 stacking pairs defined.
    Time for finding SS restraints: 6.82
  Creating SS restraints...
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.633A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 121
      removed outlier: 3.756A  pdb=" N   ALA D 104 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.074A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
      removed outlier: 3.536A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 100 through 121
      removed outlier: 3.699A  pdb=" N   ALA H 104 " --> pdb=" O   PRO H 100 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 68 through 73
      removed outlier: 4.203A  pdb=" N   ASN K  73 " --> pdb=" O   GLU K  69 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 85 through 89
      removed outlier: 4.156A  pdb=" N   ASP K  89 " --> pdb=" O   SER K  86 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 101 through 124
    Processing helix  chain 'L' and resid 101 through 124
    Processing helix  chain 'A' and resid 44 through 55
      removed outlier: 3.654A  pdb=" N   LEU A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 75
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.537A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.608A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.521A  pdb=" N   LEU E 109 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
    Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 46
      removed outlier: 7.414A  pdb=" N   ARG B  45 " --> pdb=" O   ILE A 119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.577A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.308A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'F' and resid 45 through 46
      removed outlier: 7.339A  pdb=" N   ARG F  45 " --> pdb=" O   ILE E 119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'F' and resid 80 through 81
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.270A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 58 through 60
      removed outlier: 5.534A  pdb=" N   ILE K  27 " --> pdb=" O   HIS K  80 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   HIS K  80 " --> pdb=" O   ILE K  27 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 58 through 60
      removed outlier: 3.574A  pdb=" N   LEU K  15 " --> pdb=" O   ARG K  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 59 through 60
      removed outlier: 6.410A  pdb=" N   PHE L  78 " --> pdb=" O   LEU L  28 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   ILE L  30 " --> pdb=" O   CYS L  76 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   CYS L  76 " --> pdb=" O   ILE L  30 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 59 through 60
      removed outlier: 3.621A  pdb=" N   LEU L  21 " --> pdb=" O   HIS L  18 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   LEU L  15 " --> pdb=" O   ARG L  98 " (cutoff:3.500A)

    496 hydrogen bonds defined for protein.
    1425 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      371 hydrogen bonds
      730 hydrogen bond angles
      0 basepair planarities
      146 basepair parallelities
      259 stacking parallelities
  Total time for adding SS restraints: 5.04

  Time building geometry restraints manager: 3.90 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2586
        1.33 -     1.45: 4718
        1.45 -     1.57: 6860
        1.57 -     1.69: 602
        1.69 -     1.81: 37
  Bond restraints: 14803
  Sorted by residual:
  bond pdb=" C   GLY K  19 "
       pdb=" N   PRO K  20 "
    ideal  model  delta    sigma   weight residual
    1.331  1.344 -0.012 7.90e-03 1.60e+04 2.34e+00
  bond pdb=" C3'  DG I  20 "
       pdb=" O3'  DG I  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.61e+00
  bond pdb=" CD  M3L A  36 "
       pdb=" CE  M3L A  36 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 2.00e-02 2.50e+03 1.27e+00
  bond pdb=" N   M3L A  36 "
       pdb=" CA  M3L A  36 "
    ideal  model  delta    sigma   weight residual
    1.458  1.441  0.017 1.90e-02 2.77e+03 8.47e-01
  bond pdb=" C3'  DC I  21 "
       pdb=" C2'  DC I  21 "
    ideal  model  delta    sigma   weight residual
    1.525  1.543 -0.018 2.00e-02 2.50e+03 7.99e-01
  ... (remaining 14798 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 21113
        2.29 -     4.57: 153
        4.57 -     6.86: 10
        6.86 -     9.14: 1
        9.14 -    11.43: 1
  Bond angle restraints: 21278
  Sorted by residual:
  angle pdb=" CB  MET K  37 "
        pdb=" CG  MET K  37 "
        pdb=" SD  MET K  37 "
      ideal   model   delta    sigma   weight residual
     112.70  124.13  -11.43 3.00e+00 1.11e-01 1.45e+01
  angle pdb=" CA  MET K  37 "
        pdb=" CB  MET K  37 "
        pdb=" CG  MET K  37 "
      ideal   model   delta    sigma   weight residual
     114.10  120.61   -6.51 2.00e+00 2.50e-01 1.06e+01
  angle pdb=" C   THR F  30 "
        pdb=" N   LYS F  31 "
        pdb=" CA  LYS F  31 "
      ideal   model   delta    sigma   weight residual
     120.09  123.79   -3.70 1.25e+00 6.40e-01 8.78e+00
  angle pdb=" CA  GLU K  24 "
        pdb=" CB  GLU K  24 "
        pdb=" CG  GLU K  24 "
      ideal   model   delta    sigma   weight residual
     114.10  119.14   -5.04 2.00e+00 2.50e-01 6.34e+00
  angle pdb=" CG  MET L  22 "
        pdb=" SD  MET L  22 "
        pdb=" CE  MET L  22 "
      ideal   model   delta    sigma   weight residual
     100.90   95.78    5.12 2.20e+00 2.07e-01 5.41e+00
  ... (remaining 21273 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.03: 6354
       31.03 -    62.05: 1732
       62.05 -    93.08: 41
       93.08 -   124.10: 0
      124.10 -   155.13: 1
  Dihedral angle restraints: 8128
    sinusoidal: 5321
      harmonic: 2807
  Sorted by residual:
  dihedral pdb=" C4'  DG I  20 "
           pdb=" C3'  DG I  20 "
           pdb=" O3'  DG I  20 "
           pdb=" P    DC I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   64.87  155.13     1      3.50e+01 8.16e-04 1.49e+01
  dihedral pdb=" CB  GLU L 124 "
           pdb=" CG  GLU L 124 "
           pdb=" CD  GLU L 124 "
           pdb=" OE1 GLU L 124 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.34   88.34     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CA  PHE L  17 "
           pdb=" C   PHE L  17 "
           pdb=" N   HIS L  18 "
           pdb=" CA  HIS L  18 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.12   15.88     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 8125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1532
       0.027 -    0.055: 598
       0.055 -    0.082: 184
       0.082 -    0.110: 62
       0.110 -    0.137: 12
  Chirality restraints: 2388
  Sorted by residual:
  chirality pdb=" CA  ILE B  29 "
            pdb=" N   ILE B  29 "
            pdb=" C   ILE B  29 "
            pdb=" CB  ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.72e-01
  chirality pdb=" CA  ILE F  29 "
            pdb=" N   ILE F  29 "
            pdb=" C   ILE F  29 "
            pdb=" CB  ILE F  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.45e-01
  chirality pdb=" CA  ILE L  67 "
            pdb=" N   ILE L  67 "
            pdb=" C   ILE L  67 "
            pdb=" CB  ILE L  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.99e-01
  ... (remaining 2385 not shown)

  Planarity restraints: 1642
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  63 "    0.009 2.00e-02 2.50e+03   1.80e-02 3.23e+00
        pdb=" C   GLU B  63 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   GLU B  63 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ASN B  64 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.024 2.00e-02 2.50e+03   1.07e-02 3.15e+00
        pdb=" N9   DA I -35 "    0.024 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "   -0.024 2.00e-02 2.50e+03   1.02e-02 3.11e+00
        pdb=" N9   DG I  47 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "    0.001 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DG I  47 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1639 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.70: 556
        2.70 -     3.25: 11891
        3.25 -     3.80: 26384
        3.80 -     4.35: 33394
        4.35 -     4.90: 47488
  Nonbonded interactions: 119713
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  70 "
            pdb=" N2   DG J -70 "
     model   vdw
     2.155 2.496
  nonbonded pdb=" OH  TYR L  81 "
            pdb=" OE1 GLU L  90 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" O2   DC I -50 "
            pdb=" N2   DG J  50 "
     model   vdw
     2.194 2.496
  nonbonded pdb=" O   ALA K  99 "
            pdb=" ND2 ASN K 104 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.213 3.040
  ... (remaining 119708 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 36 through 109 or (resid 110 through 111 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 112 through 134))
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 23 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'K'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.360
  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:          0.570
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     37.060
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
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      :  0.003   0.038  14803  Z= 0.158
  Angle     :  0.567  11.427  21278  Z= 0.338
  Chirality :  0.034   0.137   2388
  Planarity :  0.005   0.042   1642
  Dihedral  : 26.984 155.126   6316
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 14.62 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.26), residues: 940
  helix:  1.01 (0.21), residues: 586
  sheet:  0.29 (1.30), residues: 20
  loop : -1.63 (0.28), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP K  88 
 HIS   0.004   0.001   HIS F  75 
 PHE   0.008   0.001   PHE D  67 
 TYR   0.021   0.001   TYR L  23 
 ARG   0.005   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11448 (  855)
  hydrogen bonds       : angle       4.07865 ( 2155)
  covalent geometry    : bond        0.00339 (14803)
  covalent geometry    : angle       0.56658 (21278)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 109
  time to evaluate  : 1.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 LYS cc_start: 0.8329 (tttp) cc_final: 0.8125 (tttt)
REVERT: D  105 LYS cc_start: 0.8014 (mtpm) cc_final: 0.7791 (mtpp)
REVERT: H   44 GLN cc_start: 0.8067 (mt0) cc_final: 0.7730 (mt0)
REVERT: K   37 MET cc_start: 0.3006 (ppp) cc_final: 0.2134 (tmm)
REVERT: K  103 GLU cc_start: 0.3359 (pp20) cc_final: 0.2243 (tp30)
REVERT: L   22 MET cc_start: 0.1646 (pmm) cc_final: 0.1049 (pmm)
  outliers start: 3
  outliers final: 2
  residues processed: 111
  average time/residue: 1.9059
  time to fit residues: 224.7572
Evaluate side-chains
  102 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain K residue   67 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 92 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 49 optimal weight:    0.5980
   chunk 95 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 110 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
H  81 ASN
K  80 HIS
** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.136504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.096088 restraints weight = 19727.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.07
r_work: 0.2898 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.0638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14803  Z= 0.185
  Angle     :  0.577   8.111  21278  Z= 0.343
  Chirality :  0.036   0.128   2388
  Planarity :  0.005   0.046   1642
  Dihedral  : 30.009 156.166   4384
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.75 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.26), residues: 940
  helix:  1.62 (0.20), residues: 596
  sheet:  0.69 (1.23), residues: 20
  loop : -1.39 (0.29), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP K  91 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.009   0.001   PHE D  67 
 TYR   0.014   0.002   TYR L  23 
 ARG   0.007   0.001   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05459 (  855)
  hydrogen bonds       : angle       3.14174 ( 2155)
  covalent geometry    : bond        0.00411 (14803)
  covalent geometry    : angle       0.57678 (21278)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 1.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   44 GLN cc_start: 0.8125 (mt0) cc_final: 0.7876 (mt0)
REVERT: K   37 MET cc_start: 0.3595 (ppp) cc_final: 0.2540 (tmm)
REVERT: L   22 MET cc_start: 0.1520 (pmm) cc_final: 0.0729 (pmm)
REVERT: E  120 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8354 (mtt)
  outliers start: 16
  outliers final: 6
  residues processed: 111
  average time/residue: 1.9284
  time to fit residues: 227.6392
Evaluate side-chains
  102 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 1.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  120 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 116 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 34 optimal weight:    3.9990
   chunk 100 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 117 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.136904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.095047 restraints weight = 19843.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 1.08
r_work: 0.2898 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2779 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.0708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14803  Z= 0.164
  Angle     :  0.558   6.883  21278  Z= 0.334
  Chirality :  0.035   0.127   2388
  Planarity :  0.004   0.043   1642
  Dihedral  : 29.998 156.386   4384
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.50 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.26), residues: 940
  helix:  1.94 (0.21), residues: 596
  sheet:  0.81 (1.20), residues: 20
  loop : -1.32 (0.30), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP K  91 
 HIS   0.003   0.001   HIS H  79 
 PHE   0.015   0.001   PHE K  77 
 TYR   0.010   0.001   TYR L  38 
 ARG   0.005   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05139 (  855)
  hydrogen bonds       : angle       3.09400 ( 2155)
  covalent geometry    : bond        0.00358 (14803)
  covalent geometry    : angle       0.55785 (21278)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   44 GLN cc_start: 0.8162 (mt0) cc_final: 0.7814 (mt0)
REVERT: K  108 LYS cc_start: 0.0829 (OUTLIER) cc_final: 0.0369 (mtmm)
REVERT: L   22 MET cc_start: 0.1432 (pmm) cc_final: 0.0664 (pmm)
REVERT: L   94 TYR cc_start: 0.3605 (OUTLIER) cc_final: 0.3067 (t80)
REVERT: E   90 MET cc_start: 0.7834 (mmm) cc_final: 0.7597 (mmm)
REVERT: E  120 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8386 (mtt)
  outliers start: 19
  outliers final: 9
  residues processed: 107
  average time/residue: 1.9023
  time to fit residues: 216.5688
Evaluate side-chains
  106 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain K residue  108 LYS
Chi-restraints excluded: chain L residue   94 TYR
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  120 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 47 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 121 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 108 optimal weight:    0.8980
   chunk 85 optimal weight:    0.3980
   chunk 64 optimal weight:    3.9990
   chunk 90 optimal weight:   10.0000
   chunk 98 optimal weight:    6.9990
   chunk 110 optimal weight:    0.8980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.137430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.095784 restraints weight = 19837.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 1.08
r_work: 0.2898 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.0854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14803  Z= 0.159
  Angle     :  0.541   6.395  21278  Z= 0.326
  Chirality :  0.034   0.128   2388
  Planarity :  0.004   0.047   1642
  Dihedral  : 29.921 156.624   4384
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 15.24 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.27), residues: 940
  helix:  2.25 (0.21), residues: 593
  sheet:  0.69 (1.15), residues: 20
  loop : -1.15 (0.30), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP K  91 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.022   0.001   PHE K  77 
 TYR   0.011   0.001   TYR L  23 
 ARG   0.008   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04890 (  855)
  hydrogen bonds       : angle       2.98386 ( 2155)
  covalent geometry    : bond        0.00347 (14803)
  covalent geometry    : angle       0.54141 (21278)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   84 MET cc_start: 0.9016 (tpp) cc_final: 0.8667 (mmm)
REVERT: H   31 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.6887 (tttp)
REVERT: H   44 GLN cc_start: 0.8112 (mt0) cc_final: 0.7812 (mt0)
REVERT: K  108 LYS cc_start: 0.0774 (OUTLIER) cc_final: 0.0342 (mtmm)
REVERT: L   22 MET cc_start: 0.1337 (pmm) cc_final: 0.0518 (pmm)
REVERT: L   94 TYR cc_start: 0.3573 (OUTLIER) cc_final: 0.3065 (t80)
REVERT: A   64 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.7762 (mmtp)
REVERT: E  120 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8360 (mtt)
  outliers start: 24
  outliers final: 13
  residues processed: 113
  average time/residue: 1.8056
  time to fit residues: 217.8054
Evaluate side-chains
  115 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain G residue   41 GLU
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain H residue   31 LYS
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain K residue   75 LYS
Chi-restraints excluded: chain K residue  108 LYS
Chi-restraints excluded: chain L residue   76 CYS
Chi-restraints excluded: chain L residue   94 TYR
Chi-restraints excluded: chain A residue   37 LYS
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  120 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 97 optimal weight:   20.0000
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 86 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.136549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.095041 restraints weight = 19880.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 1.13
r_work: 0.2877 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.0997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14803  Z= 0.180
  Angle     :  0.561   6.882  21278  Z= 0.334
  Chirality :  0.036   0.127   2388
  Planarity :  0.004   0.045   1642
  Dihedral  : 30.028 156.706   4384
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 15.86 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.27), residues: 940
  helix:  2.21 (0.21), residues: 596
  sheet:  0.86 (1.16), residues: 20
  loop : -1.10 (0.30), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP K  91 
 HIS   0.004   0.001   HIS E  39 
 PHE   0.009   0.001   PHE K  17 
 TYR   0.012   0.001   TYR D 118 
 ARG   0.009   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05157 (  855)
  hydrogen bonds       : angle       2.98477 ( 2155)
  covalent geometry    : bond        0.00401 (14803)
  covalent geometry    : angle       0.56138 (21278)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   84 MET cc_start: 0.9034 (tpp) cc_final: 0.8665 (mmm)
REVERT: H   31 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.6841 (tttp)
REVERT: H   44 GLN cc_start: 0.8121 (mt0) cc_final: 0.7771 (mt0)
REVERT: K  104 ASN cc_start: 0.3105 (OUTLIER) cc_final: 0.2454 (t0)
REVERT: K  108 LYS cc_start: 0.0773 (OUTLIER) cc_final: 0.0363 (mtmm)
REVERT: L   22 MET cc_start: 0.1344 (pmm) cc_final: 0.0588 (pmm)
REVERT: L   94 TYR cc_start: 0.3654 (OUTLIER) cc_final: 0.3148 (t80)
  outliers start: 27
  outliers final: 12
  residues processed: 117
  average time/residue: 1.9043
  time to fit residues: 237.0248
Evaluate side-chains
  111 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain H residue   31 LYS
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain K residue  104 ASN
Chi-restraints excluded: chain K residue  108 LYS
Chi-restraints excluded: chain L residue   76 CYS
Chi-restraints excluded: chain L residue   94 TYR
Chi-restraints excluded: chain A residue   37 LYS
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 84 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 121 optimal weight:    0.7980
   chunk 96 optimal weight:    7.9990
   chunk 64 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 5 optimal weight:    0.4980
   chunk 112 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.136156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.094436 restraints weight = 20116.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 1.13
r_work: 0.2871 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.1100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14803  Z= 0.188
  Angle     :  0.565   6.892  21278  Z= 0.337
  Chirality :  0.036   0.130   2388
  Planarity :  0.004   0.045   1642
  Dihedral  : 30.091 156.806   4384
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.98 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.27), residues: 940
  helix:  2.21 (0.21), residues: 596
  sheet:  0.84 (1.14), residues: 20
  loop : -1.03 (0.30), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP K  91 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.007   0.001   PHE H  67 
 TYR   0.013   0.001   TYR D 118 
 ARG   0.008   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05227 (  855)
  hydrogen bonds       : angle       2.95936 ( 2155)
  covalent geometry    : bond        0.00422 (14803)
  covalent geometry    : angle       0.56507 (21278)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   31 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.6853 (tttp)
REVERT: H   44 GLN cc_start: 0.8163 (mt0) cc_final: 0.7830 (mt0)
REVERT: K  104 ASN cc_start: 0.3193 (OUTLIER) cc_final: 0.2516 (t0)
REVERT: K  108 LYS cc_start: 0.0840 (OUTLIER) cc_final: 0.0366 (mtmm)
REVERT: L   94 TYR cc_start: 0.3614 (OUTLIER) cc_final: 0.3077 (t80)
  outliers start: 22
  outliers final: 12
  residues processed: 112
  average time/residue: 1.8164
  time to fit residues: 216.8078
Evaluate side-chains
  113 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain H residue   31 LYS
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain K residue  104 ASN
Chi-restraints excluded: chain K residue  108 LYS
Chi-restraints excluded: chain L residue   76 CYS
Chi-restraints excluded: chain L residue   94 TYR
Chi-restraints excluded: chain A residue   37 LYS
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   87 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 85 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 81 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.136275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.094573 restraints weight = 19993.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.12
r_work: 0.2879 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2759 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.1115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14803  Z= 0.186
  Angle     :  0.566   6.886  21278  Z= 0.337
  Chirality :  0.036   0.129   2388
  Planarity :  0.004   0.046   1642
  Dihedral  : 30.089 156.757   4384
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.35 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.27), residues: 940
  helix:  2.21 (0.21), residues: 596
  sheet:  0.97 (1.14), residues: 20
  loop : -0.99 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  91 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.009   0.001   PHE D  67 
 TYR   0.015   0.002   TYR D 118 
 ARG   0.007   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05206 (  855)
  hydrogen bonds       : angle       2.96082 ( 2155)
  covalent geometry    : bond        0.00418 (14803)
  covalent geometry    : angle       0.56608 (21278)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   31 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.6849 (tttp)
REVERT: H   44 GLN cc_start: 0.8162 (mt0) cc_final: 0.7822 (mt0)
REVERT: K  104 ASN cc_start: 0.3221 (OUTLIER) cc_final: 0.2549 (t0)
REVERT: K  108 LYS cc_start: 0.0864 (OUTLIER) cc_final: 0.0373 (mtmm)
REVERT: L   94 TYR cc_start: 0.3621 (OUTLIER) cc_final: 0.3363 (t80)
  outliers start: 22
  outliers final: 11
  residues processed: 111
  average time/residue: 1.7713
  time to fit residues: 209.4004
Evaluate side-chains
  110 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain H residue   31 LYS
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain K residue  104 ASN
Chi-restraints excluded: chain K residue  108 LYS
Chi-restraints excluded: chain L residue   94 TYR
Chi-restraints excluded: chain A residue   37 LYS
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   87 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 118 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 102 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 117 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9980
   chunk 88 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.135747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.095107 restraints weight = 19828.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 1.08
r_work: 0.2882 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.1204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  14803  Z= 0.205
  Angle     :  0.586   7.235  21278  Z= 0.346
  Chirality :  0.037   0.130   2388
  Planarity :  0.005   0.045   1642
  Dihedral  : 30.187 156.609   4384
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.72 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.27), residues: 940
  helix:  2.12 (0.21), residues: 596
  sheet:  1.00 (1.15), residues: 20
  loop : -0.99 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  91 
 HIS   0.005   0.001   HIS E  39 
 PHE   0.008   0.001   PHE H  67 
 TYR   0.016   0.002   TYR D 118 
 ARG   0.009   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05441 (  855)
  hydrogen bonds       : angle       3.01326 ( 2155)
  covalent geometry    : bond        0.00464 (14803)
  covalent geometry    : angle       0.58560 (21278)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 1.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   95 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7759 (mtt-85)
REVERT: H   31 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.6985 (mmpt)
REVERT: H   44 GLN cc_start: 0.8186 (mt0) cc_final: 0.7871 (mt0)
REVERT: K  104 ASN cc_start: 0.3218 (OUTLIER) cc_final: 0.2464 (t0)
REVERT: K  108 LYS cc_start: 0.1014 (OUTLIER) cc_final: 0.0449 (mtmm)
REVERT: L   94 TYR cc_start: 0.3613 (OUTLIER) cc_final: 0.3388 (t80)
  outliers start: 19
  outliers final: 12
  residues processed: 111
  average time/residue: 1.8618
  time to fit residues: 219.9799
Evaluate side-chains
  114 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain D residue  119 THR
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain H residue   31 LYS
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain K residue  104 ASN
Chi-restraints excluded: chain K residue  108 LYS
Chi-restraints excluded: chain L residue   76 CYS
Chi-restraints excluded: chain L residue   94 TYR
Chi-restraints excluded: chain A residue   37 LYS
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   87 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 121 optimal weight:    0.5980
   chunk 115 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 108 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 107 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 87 optimal weight:    0.0970
   chunk 118 optimal weight:    0.9980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.136624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.095328 restraints weight = 19691.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.04
r_work: 0.2900 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14803  Z= 0.153
  Angle     :  0.566   7.667  21278  Z= 0.338
  Chirality :  0.035   0.208   2388
  Planarity :  0.004   0.046   1642
  Dihedral  : 30.175 156.231   4384
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.09 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.27), residues: 940
  helix:  2.28 (0.21), residues: 596
  sheet:  0.96 (1.16), residues: 20
  loop : -0.93 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K  91 
 HIS   0.003   0.001   HIS H  79 
 PHE   0.006   0.001   PHE F  61 
 TYR   0.013   0.001   TYR D 118 
 ARG   0.010   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05042 (  855)
  hydrogen bonds       : angle       3.01377 ( 2155)
  covalent geometry    : bond        0.00332 (14803)
  covalent geometry    : angle       0.56619 (21278)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   92 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8427 (ptm160)
REVERT: B   95 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7711 (mtt-85)
REVERT: H   31 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.6991 (mmpt)
REVERT: H   44 GLN cc_start: 0.8156 (mt0) cc_final: 0.7802 (mt0)
REVERT: K  104 ASN cc_start: 0.3160 (OUTLIER) cc_final: 0.2456 (t0)
REVERT: K  108 LYS cc_start: 0.1021 (OUTLIER) cc_final: 0.0503 (mtmm)
REVERT: L   94 TYR cc_start: 0.3612 (OUTLIER) cc_final: 0.3390 (t80)
  outliers start: 19
  outliers final: 9
  residues processed: 112
  average time/residue: 1.8699
  time to fit residues: 222.9922
Evaluate side-chains
  112 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain H residue   31 LYS
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain K residue  104 ASN
Chi-restraints excluded: chain K residue  108 LYS
Chi-restraints excluded: chain L residue   94 TYR
Chi-restraints excluded: chain A residue   37 LYS
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 117 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 108 optimal weight:    0.5980
   chunk 62 optimal weight:    3.9990
   chunk 85 optimal weight:    7.9990
   chunk 31 optimal weight:    0.7980
   chunk 103 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.136401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.094999 restraints weight = 19806.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 1.05
r_work: 0.2897 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.1212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14803  Z= 0.176
  Angle     :  0.569   8.102  21278  Z= 0.337
  Chirality :  0.036   0.141   2388
  Planarity :  0.004   0.052   1642
  Dihedral  : 30.112 156.575   4384
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 18.71 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.27), residues: 940
  helix:  2.24 (0.21), residues: 596
  sheet:  1.08 (1.17), residues: 20
  loop : -0.89 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP K  84 
 HIS   0.003   0.001   HIS H  79 
 PHE   0.006   0.001   PHE D  67 
 TYR   0.015   0.002   TYR D 118 
 ARG   0.010   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05133 (  855)
  hydrogen bonds       : angle       2.98122 ( 2155)
  covalent geometry    : bond        0.00393 (14803)
  covalent geometry    : angle       0.56884 (21278)

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 1.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   92 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8440 (ptm160)
REVERT: B   95 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7720 (mtt-85)
REVERT: H   31 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.6998 (mmpt)
REVERT: H   44 GLN cc_start: 0.8162 (mt0) cc_final: 0.7844 (mt0)
REVERT: K  104 ASN cc_start: 0.3204 (OUTLIER) cc_final: 0.2502 (t0)
REVERT: K  108 LYS cc_start: 0.1014 (OUTLIER) cc_final: 0.0490 (mtmm)
REVERT: L   94 TYR cc_start: 0.3609 (OUTLIER) cc_final: 0.3391 (t80)
  outliers start: 15
  outliers final: 9
  residues processed: 108
  average time/residue: 1.9521
  time to fit residues: 224.1014
Evaluate side-chains
  112 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue  116 THR
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain H residue   31 LYS
Chi-restraints excluded: chain H residue  113 LYS
Chi-restraints excluded: chain K residue   67 ILE
Chi-restraints excluded: chain K residue  104 ASN
Chi-restraints excluded: chain K residue  108 LYS
Chi-restraints excluded: chain L residue   94 TYR
Chi-restraints excluded: chain A residue   37 LYS
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 84 optimal weight:   10.0000
   chunk 50 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 111 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 81 optimal weight:    4.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.136017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.095426 restraints weight = 19901.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 1.08
r_work: 0.2886 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2764 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14803  Z= 0.194
  Angle     :  0.580   8.788  21278  Z= 0.342
  Chirality :  0.037   0.131   2388
  Planarity :  0.005   0.048   1642
  Dihedral  : 30.128 156.545   4384
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 18.46 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.27), residues: 940
  helix:  2.17 (0.21), residues: 596
  sheet:  1.24 (1.17), residues: 20
  loop : -0.89 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP K  84 
 HIS   0.004   0.001   HIS E  39 
 PHE   0.007   0.001   PHE H  67 
 TYR   0.017   0.002   TYR D 118 
 ARG   0.009   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05306 (  855)
  hydrogen bonds       : angle       3.00479 ( 2155)
  covalent geometry    : bond        0.00437 (14803)
  covalent geometry    : angle       0.57954 (21278)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10826.37 seconds
wall clock time: 185 minutes 54.96 seconds (11154.96 seconds total)