Starting phenix.real_space_refine
on Sun Jun 15 19:08:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xd0_33131/06_2025/7xd0_33131.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xd0_33131/06_2025/7xd0_33131.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xd0_33131/06_2025/7xd0_33131.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xd0_33131/06_2025/7xd0_33131.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xd0_33131/06_2025/7xd0_33131.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xd0_33131/06_2025/7xd0_33131.cif"
  }
  resolution = 3.48
  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
  Anisotropic ADP refinement not supported. Converting 5986 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     292      5.49       5
     S      14      5.16       5
     C    7398      2.51       5
     N    2466      2.21       5
     O    3052      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13222
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "F"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 657
          Classifications: {'peptide': 83}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 80}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "G"
      Number of atoms: 831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 831
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "H"
      Number of atoms: 718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 718
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 805
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 811
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 718
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "C"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "B"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 657
          Classifications: {'peptide': 83}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "I"
      Number of atoms: 2975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 2975
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "J"
      Number of atoms: 3011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3011
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "L"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "K"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
  Residues with excluded nonbonded symmetry interactions: 8
    residue:
      pdb=" N   LEU L  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU L  73 " occ=0.45
    residue:
      pdb=" N   ARG L  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG L  74 " occ=0.45
    residue:
      pdb=" N   GLY L  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY L  75 " occ=0.25
    residue:
      pdb=" N   GLY L  76 " occ=0.25
      ... (3 atoms not shown)
      pdb=" OXT GLY L  76 " occ=0.25
    residue:
      pdb=" N   LEU K  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU K  73 " occ=0.45
    residue:
      pdb=" N   ARG K  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG K  74 " occ=0.45
    residue:
      pdb=" N   GLY K  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY K  75 " occ=0.25
    residue:
      pdb=" N   GLY K  76 " occ=0.25
      ... (3 atoms not shown)
      pdb=" OXT GLY K  76 " occ=0.25
  Time building chain proxies: 7.84, per 1000 atoms: 0.59
  Number of scatterers: 13222
  At special positions: 0
  Unit cell: (139.62, 136.398, 93.438, 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     292     15.00
     O    3052      8.00
     N    2466      7.00
     C    7398      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: 3.07
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1706

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 9 sheets defined
      60.0% alpha, 6.1% beta
      141 base pairs and 244 stacking pairs defined.
    Time for finding SS restraints: 6.08
  Creating SS restraints...
    Processing helix  chain 'F' and resid 30 through 35
    Processing helix  chain 'F' and resid 37 through 42
    Processing helix  chain 'F' and resid 49 through 57
      removed outlier: 3.753A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 87
      removed outlier: 3.533A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.467A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
      removed outlier: 3.660A  pdb=" N   LEU G  96 " --> pdb=" O   GLU G  92 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 124
      removed outlier: 3.834A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ALA H 124 " --> pdb=" O   LYS H 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
      removed outlier: 3.863A  pdb=" N   LEU E  48 " --> pdb=" O   GLY E  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.565A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 124
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.384A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.525A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.933A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
      removed outlier: 3.651A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 22 through 35
      removed outlier: 3.506A  pdb=" N   LYS L  27 " --> pdb=" O   ILE L  23 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLN L  31 " --> pdb=" O   LYS L  27 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 37 through 39
      No H-bonds generated for 'chain 'L' and resid 37 through 39'
    Processing helix  chain 'K' and resid 22 through 35
      removed outlier: 3.507A  pdb=" N   LYS K  27 " --> pdb=" O   ILE K  23 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLN K  31 " --> pdb=" O   LYS K  27 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 37 through 39
      No H-bonds generated for 'chain 'K' and resid 37 through 39'
    Processing sheet with id=AA1, first strand: chain 'F' and resid 45 through 46
      removed outlier: 7.530A  pdb=" N   ARG F  45 " --> pdb=" O   ILE E 119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'F' and resid 96 through 98
      removed outlier: 5.985A  pdb=" N   THR F  96 " --> pdb=" O   THR C 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.489A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'G' and resid 100 through 102
    Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 54
      removed outlier: 7.731A  pdb=" N   GLY D  53 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'D' and resid 88 through 89
    Processing sheet with id=AA8, first strand: chain 'L' and resid 12 through 16
      removed outlier: 3.598A  pdb=" N   PHE L  45 " --> pdb=" O   LYS L  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'K' and resid 12 through 16
      removed outlier: 3.598A  pdb=" N   PHE K  45 " --> pdb=" O   LYS K  48 " (cutoff:3.500A)

    407 hydrogen bonds defined for protein.
    1203 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      360 hydrogen bonds
      712 hydrogen bond angles
      0 basepair planarities
      141 basepair parallelities
      244 stacking parallelities
  Total time for adding SS restraints: 4.40

  Time building geometry restraints manager: 3.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2876
        1.33 -     1.45: 4188
        1.45 -     1.57: 6370
        1.57 -     1.69: 582
        1.69 -     1.81: 26
  Bond restraints: 14042
  Sorted by residual:
  bond pdb=" C3'  DC J 126 "
       pdb=" O3'  DC J 126 "
    ideal  model  delta    sigma   weight residual
    1.422  1.466 -0.044 3.00e-02 1.11e+03 2.18e+00
  bond pdb=" C3'  DT J  15 "
       pdb=" O3'  DT J  15 "
    ideal  model  delta    sigma   weight residual
    1.422  1.465 -0.043 3.00e-02 1.11e+03 2.06e+00
  bond pdb=" N   THR F  71 "
       pdb=" CA  THR F  71 "
    ideal  model  delta    sigma   weight residual
    1.456  1.471 -0.015 1.23e-02 6.61e+03 1.47e+00
  bond pdb=" N   ILE F  29 "
       pdb=" CA  ILE F  29 "
    ideal  model  delta    sigma   weight residual
    1.474  1.457  0.018 1.57e-02 4.06e+03 1.27e+00
  bond pdb=" CA  ASP H  51 "
       pdb=" C   ASP H  51 "
    ideal  model  delta    sigma   weight residual
    1.526  1.538 -0.011 1.03e-02 9.43e+03 1.17e+00
  ... (remaining 14037 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 19395
        1.31 -     2.63: 730
        2.63 -     3.94: 64
        3.94 -     5.26: 19
        5.26 -     6.57: 5
  Bond angle restraints: 20213
  Sorted by residual:
  angle pdb=" N   ASP F  68 "
        pdb=" CA  ASP F  68 "
        pdb=" C   ASP F  68 "
      ideal   model   delta    sigma   weight residual
     112.93  108.08    4.85 1.33e+00 5.65e-01 1.33e+01
  angle pdb=" C   VAL F  70 "
        pdb=" N   THR F  71 "
        pdb=" CA  THR F  71 "
      ideal   model   delta    sigma   weight residual
     126.45  132.68   -6.23 1.77e+00 3.19e-01 1.24e+01
  angle pdb=" OG1 THR F  71 "
        pdb=" CB  THR F  71 "
        pdb=" CG2 THR F  71 "
      ideal   model   delta    sigma   weight residual
     109.30  102.73    6.57 2.00e+00 2.50e-01 1.08e+01
  angle pdb=" C   PHE F 100 "
        pdb=" N   GLY F 101 "
        pdb=" CA  GLY F 101 "
      ideal   model   delta    sigma   weight residual
     121.70  127.18   -5.48 1.80e+00 3.09e-01 9.27e+00
  angle pdb=" CA  ARG F  67 "
        pdb=" C   ARG F  67 "
        pdb=" N   ASP F  68 "
      ideal   model   delta    sigma   weight residual
     118.87  115.37    3.50 1.18e+00 7.18e-01 8.82e+00
  ... (remaining 20208 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.47: 6275
       34.47 -    68.93: 1416
       68.93 -   103.40: 30
      103.40 -   137.87: 0
      137.87 -   172.33: 3
  Dihedral angle restraints: 7724
    sinusoidal: 5081
      harmonic: 2643
  Sorted by residual:
  dihedral pdb=" CA  THR F  71 "
           pdb=" C   THR F  71 "
           pdb=" N   TYR F  72 "
           pdb=" CA  TYR F  72 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.64   27.36     0      5.00e+00 4.00e-02 2.99e+01
  dihedral pdb=" CA  ALA F  89 "
           pdb=" C   ALA F  89 "
           pdb=" N   LEU F  90 "
           pdb=" CA  LEU F  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.90   27.10     0      5.00e+00 4.00e-02 2.94e+01
  dihedral pdb=" CA  ALA F  69 "
           pdb=" C   ALA F  69 "
           pdb=" N   VAL F  70 "
           pdb=" CA  VAL F  70 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.59   22.41     0      5.00e+00 4.00e-02 2.01e+01
  ... (remaining 7721 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1759
       0.036 -    0.072: 422
       0.072 -    0.109: 96
       0.109 -    0.145: 32
       0.145 -    0.181: 2
  Chirality restraints: 2311
  Sorted by residual:
  chirality pdb=" CB  THR F  71 "
            pdb=" CA  THR F  71 "
            pdb=" OG1 THR F  71 "
            pdb=" CG2 THR F  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.73   -0.18 2.00e-01 2.50e+01 8.18e-01
  chirality pdb=" CA  PHE F 100 "
            pdb=" N   PHE F 100 "
            pdb=" C   PHE F 100 "
            pdb=" CB  PHE F 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.58e-01
  chirality pdb=" CA  ARG L  42 "
            pdb=" N   ARG L  42 "
            pdb=" C   ARG L  42 "
            pdb=" CB  ARG L  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.61e-01
  ... (remaining 2308 not shown)

  Planarity restraints: 1552
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU F  62 "    0.015 2.00e-02 2.50e+03   3.04e-02 9.23e+00
        pdb=" C   LEU F  62 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   LEU F  62 "    0.020 2.00e-02 2.50e+03
        pdb=" N   GLU F  63 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  79 "    0.030 5.00e-02 4.00e+02   4.56e-02 3.32e+00
        pdb=" N   PRO C  80 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  91 "   -0.018 2.00e-02 2.50e+03   8.14e-03 1.82e+00
        pdb=" N9   DA I  91 "    0.018 2.00e-02 2.50e+03
        pdb=" C8   DA I  91 "    0.000 2.00e-02 2.50e+03
        pdb=" N7   DA I  91 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DA I  91 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DA I  91 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  91 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1   DA I  91 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  91 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I  91 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I  91 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1549 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 154
        2.63 -     3.20: 10839
        3.20 -     3.76: 23949
        3.76 -     4.33: 31828
        4.33 -     4.90: 45569
  Nonbonded interactions: 112339
  Sorted by model distance:
  nonbonded pdb=" CG  ARG K  42 "
            pdb=" NH2 ARG K  72 "
     model   vdw
     2.062 3.520
  nonbonded pdb=" O   GLN K  62 "
            pdb=" OG  SER K  65 "
     model   vdw
     2.132 3.040
  nonbonded pdb=" O   GLN L  62 "
            pdb=" OG  SER L  65 "
     model   vdw
     2.132 3.040
  nonbonded pdb=" O2   DC I  74 "
            pdb=" N2   DG J  74 "
     model   vdw
     2.183 2.496
  nonbonded pdb=" OG1 THR D  90 "
            pdb=" OE1 GLU D  93 "
     model   vdw
     2.223 3.040
  ... (remaining 112334 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 37 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and (resid 11 through 117 or (resid 118 and (name N or name CA or nam \ 
e C or name O or name CB ))))
  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=0.25 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:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.140
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     35.050
  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:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
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   0.044  14042  Z= 0.155
  Angle     :  0.573   6.573  20213  Z= 0.346
  Chirality :  0.036   0.181   2311
  Planarity :  0.003   0.046   1552
  Dihedral  : 27.036 172.333   6018
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.39 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  1.30 (0.29), residues: 895
  helix:  1.51 (0.23), residues: 562
  sheet: -0.46 (0.79), residues: 50
  loop : -0.06 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C  31 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.018   0.002   TYR F  88 
 ARG   0.003   0.000   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11505 (  767)
  hydrogen bonds       : angle       4.80620 ( 1915)
  covalent geometry    : bond        0.00327 (14042)
  covalent geometry    : angle       0.57278 (20213)

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

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

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 140
  time to evaluate  : 1.015 
Fit side-chains
REVERT: G   61 GLU cc_start: 0.7469 (tp30) cc_final: 0.7258 (tp30)
REVERT: G   84 GLN cc_start: 0.8809 (tp40) cc_final: 0.8576 (tp40)
REVERT: H   59 MET cc_start: 0.8586 (tpp) cc_final: 0.8379 (tpp)
REVERT: H  116 LYS cc_start: 0.7879 (ttpp) cc_final: 0.7611 (ttpp)
REVERT: E   58 THR cc_start: 0.8782 (p) cc_final: 0.8523 (p)
REVERT: D   68 ASP cc_start: 0.8486 (t0) cc_final: 0.8251 (t0)
REVERT: L   74 ARG cc_start: -0.0092 (OUTLIER) cc_final: -0.0744 (mmm160)
REVERT: K    1 MET cc_start: 0.0618 (tpt) cc_final: 0.0259 (tpt)
  outliers start: 2
  outliers final: 0
  residues processed: 141
  average time/residue: 0.2759
  time to fit residues: 54.7604
Evaluate side-chains
  124 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   74 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 86 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 46 optimal weight:    0.3980
   chunk 89 optimal weight:    5.9990
   chunk 34 optimal weight:    0.5980
   chunk 54 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 103 optimal weight:    0.0020
   overall best weight:    0.5590

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  73 ASN
A 108 ASN
D  63 ASN
C  38 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  40 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.110612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.076603 restraints weight = 31743.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 2.55
r_work: 0.2912 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2911
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2911 r_free = 0.2911    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2904 r_free = 0.2904    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2904
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.1044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14042  Z= 0.143
  Angle     :  0.550   5.835  20213  Z= 0.331
  Chirality :  0.036   0.151   2311
  Planarity :  0.004   0.044   1552
  Dihedral  : 30.057 172.295   4206
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  6.67 %
    Favored  : 92.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  1.82 (0.29), residues: 895
  helix:  1.95 (0.23), residues: 570
  sheet: -0.84 (0.73), residues: 50
  loop :  0.13 (0.39), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 113 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.017   0.001   TYR H  40 
 ARG   0.003   0.000   ARG E  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04094 (  767)
  hydrogen bonds       : angle       3.36668 ( 1915)
  covalent geometry    : bond        0.00305 (14042)
  covalent geometry    : angle       0.55005 (20213)

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

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

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 146
  time to evaluate  : 1.145 
Fit side-chains
REVERT: F   25 ASN cc_start: 0.8333 (m-40) cc_final: 0.8089 (m-40)
REVERT: G   61 GLU cc_start: 0.8166 (tp30) cc_final: 0.7841 (tp30)
REVERT: H   54 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8239 (tt)
REVERT: E   58 THR cc_start: 0.8956 (p) cc_final: 0.8701 (p)
REVERT: D   89 ILE cc_start: 0.9229 (mt) cc_final: 0.8965 (mt)
REVERT: C   78 ILE cc_start: 0.8427 (mm) cc_final: 0.8214 (mm)
REVERT: B   25 ASN cc_start: 0.8914 (m110) cc_final: 0.8406 (m-40)
  outliers start: 7
  outliers final: 4
  residues processed: 150
  average time/residue: 0.2624
  time to fit residues: 55.8987
Evaluate side-chains
  131 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 126
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   38 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 109 optimal weight:   10.0000
   chunk 89 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
G  73 ASN
A 125 GLN
D  63 ASN
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
B  25 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.107734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.070035 restraints weight = 32078.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 2.84
r_work: 0.2846 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2844
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2844 r_free = 0.2844    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2844 r_free = 0.2844    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2844
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  14042  Z= 0.202
  Angle     :  0.595   6.070  20213  Z= 0.350
  Chirality :  0.038   0.176   2311
  Planarity :  0.004   0.045   1552
  Dihedral  : 30.503 172.893   4202
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  8.50 %
    Favored  : 89.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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:  1.74 (0.29), residues: 895
  helix:  1.89 (0.23), residues: 571
  sheet: -0.58 (0.72), residues: 50
  loop :  0.02 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.011   0.002   PHE A  67 
 TYR   0.021   0.002   TYR D  40 
 ARG   0.004   0.000   ARG B  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04727 (  767)
  hydrogen bonds       : angle       3.22354 ( 1915)
  covalent geometry    : bond        0.00458 (14042)
  covalent geometry    : angle       0.59454 (20213)

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

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

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 1.109 
Fit side-chains
REVERT: F   25 ASN cc_start: 0.8410 (m-40) cc_final: 0.8167 (m-40)
REVERT: G   61 GLU cc_start: 0.8070 (tp30) cc_final: 0.7855 (tp30)
REVERT: H   54 ILE cc_start: 0.8491 (mm) cc_final: 0.8277 (tt)
REVERT: D   68 ASP cc_start: 0.8700 (t0) cc_final: 0.8409 (t0)
REVERT: D  105 GLU cc_start: 0.7160 (tp30) cc_final: 0.6865 (tp30)
REVERT: D  108 LYS cc_start: 0.7981 (ttpt) cc_final: 0.7654 (ttpt)
REVERT: B   25 ASN cc_start: 0.8914 (m-40) cc_final: 0.8313 (m-40)
  outliers start: 15
  outliers final: 10
  residues processed: 135
  average time/residue: 0.2798
  time to fit residues: 53.4148
Evaluate side-chains
  131 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain B residue   63 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 113 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0980
   chunk 15 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 96 optimal weight:    5.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
G  73 ASN
A 125 GLN
D  63 ASN
D  67 ASN
C  73 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.109233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.075004 restraints weight = 31671.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 2.65
r_work: 0.2880 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2878
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2878
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14042  Z= 0.142
  Angle     :  0.543   5.881  20213  Z= 0.325
  Chirality :  0.035   0.152   2311
  Planarity :  0.003   0.045   1552
  Dihedral  : 30.225 172.452   4202
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.33 %
    Favored  : 88.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  1.98 (0.29), residues: 895
  helix:  2.08 (0.23), residues: 570
  sheet: -0.35 (0.70), residues: 52
  loop :  0.09 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.018   0.001   TYR H  40 
 ARG   0.002   0.000   ARG H  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04046 (  767)
  hydrogen bonds       : angle       3.00291 ( 1915)
  covalent geometry    : bond        0.00308 (14042)
  covalent geometry    : angle       0.54277 (20213)

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

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

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 133
  time to evaluate  : 1.122 
Fit side-chains
REVERT: F   25 ASN cc_start: 0.8408 (m-40) cc_final: 0.8133 (m-40)
REVERT: G   61 GLU cc_start: 0.8070 (tp30) cc_final: 0.7846 (tp30)
REVERT: H   54 ILE cc_start: 0.8447 (mm) cc_final: 0.8237 (tt)
REVERT: E   58 THR cc_start: 0.8907 (p) cc_final: 0.8653 (p)
REVERT: E   73 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8557 (pp20)
REVERT: D   59 MET cc_start: 0.8918 (tpp) cc_final: 0.8399 (tpp)
REVERT: D   68 ASP cc_start: 0.8687 (t0) cc_final: 0.8413 (t0)
REVERT: B   25 ASN cc_start: 0.8858 (m-40) cc_final: 0.8154 (m110)
  outliers start: 12
  outliers final: 7
  residues processed: 138
  average time/residue: 0.2732
  time to fit residues: 53.6983
Evaluate side-chains
  131 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 123
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain B residue   63 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 96 optimal weight:    5.9990
   chunk 40 optimal weight:    0.1980
   chunk 62 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
G  73 ASN
H  84 ASN
A 125 GLN
D  84 ASN
C  73 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.109947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.072432 restraints weight = 31986.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 2.96
r_work: 0.2898 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2897
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2897
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14042  Z= 0.141
  Angle     :  0.532   5.609  20213  Z= 0.319
  Chirality :  0.035   0.146   2311
  Planarity :  0.003   0.047   1552
  Dihedral  : 30.159 172.654   4202
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 10.98 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.29), residues: 895
  helix:  2.17 (0.22), residues: 570
  sheet: -0.10 (0.71), residues: 52
  loop :  0.10 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.019   0.001   TYR D  40 
 ARG   0.001   0.000   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03996 (  767)
  hydrogen bonds       : angle       2.92305 ( 1915)
  covalent geometry    : bond        0.00305 (14042)
  covalent geometry    : angle       0.53182 (20213)

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

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

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 1.067 
Fit side-chains
REVERT: F   25 ASN cc_start: 0.8321 (m-40) cc_final: 0.8027 (m-40)
REVERT: G   61 GLU cc_start: 0.8008 (tp30) cc_final: 0.7807 (tp30)
REVERT: E   58 THR cc_start: 0.8908 (p) cc_final: 0.8673 (p)
REVERT: E   73 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8402 (pp20)
REVERT: E   76 GLN cc_start: 0.8127 (tp-100) cc_final: 0.7732 (pt0)
REVERT: D   59 MET cc_start: 0.8876 (tpp) cc_final: 0.8214 (tpp)
REVERT: B   25 ASN cc_start: 0.8782 (m-40) cc_final: 0.8140 (m-40)
  outliers start: 13
  outliers final: 8
  residues processed: 138
  average time/residue: 0.2738
  time to fit residues: 53.7306
Evaluate side-chains
  133 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   71 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 103 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 58 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 75 optimal weight:    6.9990
   chunk 99 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
G  73 ASN
H  84 ASN
A 125 GLN
C  73 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.110215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.073028 restraints weight = 32543.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 2.97
r_work: 0.2911 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2908
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2908
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14042  Z= 0.144
  Angle     :  0.533   5.797  20213  Z= 0.319
  Chirality :  0.035   0.148   2311
  Planarity :  0.003   0.047   1552
  Dihedral  : 30.132 172.796   4202
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.50 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.29), residues: 895
  helix:  2.20 (0.22), residues: 570
  sheet:  0.10 (0.72), residues: 52
  loop :  0.07 (0.37), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.022   0.001   TYR D  40 
 ARG   0.002   0.000   ARG B  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04021 (  767)
  hydrogen bonds       : angle       2.89724 ( 1915)
  covalent geometry    : bond        0.00312 (14042)
  covalent geometry    : angle       0.53297 (20213)

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

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

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 1.030 
Fit side-chains
REVERT: H   80 LEU cc_start: 0.9173 (tp) cc_final: 0.8918 (tp)
REVERT: E   58 THR cc_start: 0.8922 (p) cc_final: 0.8673 (p)
REVERT: E   73 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8474 (pp20)
REVERT: E   76 GLN cc_start: 0.8108 (tp-100) cc_final: 0.7743 (pt0)
REVERT: D   59 MET cc_start: 0.8860 (tpp) cc_final: 0.8652 (tpp)
REVERT: D  108 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7672 (tttt)
REVERT: B   25 ASN cc_start: 0.8759 (m-40) cc_final: 0.8141 (m-40)
  outliers start: 13
  outliers final: 8
  residues processed: 134
  average time/residue: 0.3210
  time to fit residues: 60.6846
Evaluate side-chains
  130 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 1.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   71 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 92 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   chunk 108 optimal weight:    7.9990
   chunk 86 optimal weight:    7.9990
   chunk 49 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9980
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
G  73 ASN
H  84 ASN
A 125 GLN
C  73 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.107335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.070093 restraints weight = 31822.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 2.85
r_work: 0.2843 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2841
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  14042  Z= 0.217
  Angle     :  0.609   6.833  20213  Z= 0.355
  Chirality :  0.039   0.184   2311
  Planarity :  0.004   0.045   1552
  Dihedral  : 30.567 173.115   4202
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 11.63 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  1.79 (0.29), residues: 895
  helix:  1.91 (0.22), residues: 571
  sheet:  0.13 (0.73), residues: 52
  loop : -0.07 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS B  75 
 PHE   0.015   0.002   PHE F  61 
 TYR   0.024   0.002   TYR D  40 
 ARG   0.004   0.000   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04810 (  767)
  hydrogen bonds       : angle       3.12677 ( 1915)
  covalent geometry    : bond        0.00493 (14042)
  covalent geometry    : angle       0.60934 (20213)

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

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

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 1.005 
Fit side-chains
REVERT: F   88 TYR cc_start: 0.6524 (m-10) cc_final: 0.6254 (m-10)
REVERT: F   92 ARG cc_start: 0.8501 (tmt-80) cc_final: 0.8261 (tmt-80)
REVERT: E   73 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8476 (pp20)
REVERT: D   59 MET cc_start: 0.8869 (tpp) cc_final: 0.8290 (tpp)
REVERT: C  101 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8918 (p)
REVERT: B   25 ASN cc_start: 0.8864 (m-40) cc_final: 0.8309 (m-40)
  outliers start: 16
  outliers final: 10
  residues processed: 126
  average time/residue: 0.3603
  time to fit residues: 64.5790
Evaluate side-chains
  124 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   26 ILE
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   71 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 102 optimal weight:    7.9990
   chunk 55 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 85 optimal weight:    8.9990
   chunk 46 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 98 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
F  25 ASN
G  73 ASN
H  84 ASN
C  73 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.108546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.071525 restraints weight = 31897.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 2.91
r_work: 0.2876 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2873
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2873
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14042  Z= 0.161
  Angle     :  0.566   7.717  20213  Z= 0.334
  Chirality :  0.036   0.159   2311
  Planarity :  0.004   0.045   1552
  Dihedral  : 30.334 172.171   4202
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.07 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.29), residues: 895
  helix:  2.07 (0.23), residues: 568
  sheet:  0.51 (0.75), residues: 50
  loop : -0.12 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.010   0.001   PHE A  67 
 TYR   0.020   0.001   TYR D  40 
 ARG   0.002   0.000   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04229 (  767)
  hydrogen bonds       : angle       3.00947 ( 1915)
  covalent geometry    : bond        0.00358 (14042)
  covalent geometry    : angle       0.56559 (20213)

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

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

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 1.534 
Fit side-chains
REVERT: F   92 ARG cc_start: 0.8494 (tmt-80) cc_final: 0.8208 (tmt-80)
REVERT: E   58 THR cc_start: 0.8904 (p) cc_final: 0.8646 (p)
REVERT: E   73 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8465 (pp20)
REVERT: E   76 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7719 (pt0)
REVERT: D   59 MET cc_start: 0.8843 (tpp) cc_final: 0.8642 (tpp)
REVERT: D  108 LYS cc_start: 0.7928 (ttpt) cc_final: 0.7603 (ttpt)
REVERT: C  101 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8919 (p)
REVERT: B   25 ASN cc_start: 0.8813 (m-40) cc_final: 0.8293 (m-40)
  outliers start: 14
  outliers final: 8
  residues processed: 129
  average time/residue: 0.2956
  time to fit residues: 54.3172
Evaluate side-chains
  130 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 1.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   71 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 29 optimal weight:    0.4980
   chunk 78 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 105 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
G  73 ASN
H  84 ASN
A 125 GLN
C  73 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.108457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.071381 restraints weight = 31948.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 2.90
r_work: 0.2878 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2876
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2876
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  14042  Z= 0.170
  Angle     :  0.572   8.397  20213  Z= 0.336
  Chirality :  0.036   0.162   2311
  Planarity :  0.004   0.047   1552
  Dihedral  : 30.348 172.321   4202
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.68 %
    Favored  : 85.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  1.97 (0.29), residues: 895
  helix:  2.06 (0.23), residues: 568
  sheet:  0.67 (0.75), residues: 50
  loop : -0.13 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.011   0.002   PHE A  67 
 TYR   0.027   0.002   TYR D  40 
 ARG   0.002   0.000   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04301 (  767)
  hydrogen bonds       : angle       3.00622 ( 1915)
  covalent geometry    : bond        0.00380 (14042)
  covalent geometry    : angle       0.57164 (20213)

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

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

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 1.135 
Fit side-chains
REVERT: H   85 LYS cc_start: 0.8728 (mptt) cc_final: 0.8389 (mmtt)
REVERT: E   58 THR cc_start: 0.8921 (p) cc_final: 0.8665 (p)
REVERT: E   73 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8409 (pp20)
REVERT: E   76 GLN cc_start: 0.8083 (tp-100) cc_final: 0.7730 (pt0)
REVERT: D  108 LYS cc_start: 0.7945 (ttpt) cc_final: 0.7627 (ttpt)
REVERT: C  101 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8928 (p)
REVERT: B   25 ASN cc_start: 0.8821 (m-40) cc_final: 0.8310 (m-40)
  outliers start: 13
  outliers final: 8
  residues processed: 128
  average time/residue: 0.2807
  time to fit residues: 50.8178
Evaluate side-chains
  129 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   71 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 99 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 113 optimal weight:   20.0000
   chunk 94 optimal weight:    4.9990
   chunk 60 optimal weight:    0.0070
   chunk 72 optimal weight:    7.9990
   chunk 108 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   overall best weight:    2.4004

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

Flipped N/Q/H residues before XYZ refinement:
F  25 ASN
G  73 ASN
H  84 ASN
A 108 ASN
A 125 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.106514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.069229 restraints weight = 31915.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 2.89
r_work: 0.2820 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2818
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2818
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  14042  Z= 0.251
  Angle     :  0.651   9.251  20213  Z= 0.374
  Chirality :  0.040   0.191   2311
  Planarity :  0.004   0.044   1552
  Dihedral  : 30.712 172.667   4202
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 13.20 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  1.58 (0.28), residues: 895
  helix:  1.77 (0.22), residues: 569
  sheet:  0.58 (0.75), residues: 50
  loop : -0.33 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS B  75 
 PHE   0.017   0.002   PHE F  61 
 TYR   0.028   0.002   TYR D  40 
 ARG   0.004   0.000   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05068 (  767)
  hydrogen bonds       : angle       3.19523 ( 1915)
  covalent geometry    : bond        0.00578 (14042)
  covalent geometry    : angle       0.65141 (20213)

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

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

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1790 Ramachandran restraints generated.
    895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 1.398 
Fit side-chains
REVERT: F   88 TYR cc_start: 0.6783 (m-10) cc_final: 0.6502 (m-10)
REVERT: F   92 ARG cc_start: 0.8568 (tmt-80) cc_final: 0.8342 (tmt-80)
REVERT: E   73 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8558 (pp20)
REVERT: A   97 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8102 (mt-10)
REVERT: D   59 MET cc_start: 0.8922 (tpp) cc_final: 0.8483 (tpp)
REVERT: C  101 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8917 (p)
REVERT: B   25 ASN cc_start: 0.8884 (m-40) cc_final: 0.8494 (m-40)
  outliers start: 13
  outliers final: 9
  residues processed: 116
  average time/residue: 0.3876
  time to fit residues: 65.1058
Evaluate side-chains
  120 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 1.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   71 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0980
   chunk 60 optimal weight:    0.9990
   chunk 87 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 98 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
G  73 ASN
H  84 ASN
A 108 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.108970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.071803 restraints weight = 31939.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 2.89
r_work: 0.2891 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2889
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2889 r_free = 0.2889    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2889 r_free = 0.2889    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2889
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14042  Z= 0.146
  Angle     :  0.565   8.800  20213  Z= 0.333
  Chirality :  0.035   0.148   2311
  Planarity :  0.004   0.046   1552
  Dihedral  : 30.235 171.292   4202
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 13.86 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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:  1.97 (0.29), residues: 895
  helix:  2.07 (0.23), residues: 570
  sheet:  0.85 (0.76), residues: 50
  loop : -0.19 (0.36), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.010   0.001   PHE F 100 
 TYR   0.023   0.002   TYR D  40 
 ARG   0.003   0.000   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04078 (  767)
  hydrogen bonds       : angle       2.96820 ( 1915)
  covalent geometry    : bond        0.00316 (14042)
  covalent geometry    : angle       0.56535 (20213)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7815.89 seconds
wall clock time: 140 minutes 20.25 seconds (8420.25 seconds total)