Starting phenix.real_space_refine
on Thu Mar  5 00:36:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xd0_33131/03_2026/7xd0_33131.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xd0_33131/03_2026/7xd0_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xd0_33131/03_2026/7xd0_33131.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xd0_33131/03_2026/7xd0_33131.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xd0_33131/03_2026/7xd0_33131.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xd0_33131/03_2026/7xd0_33131.map"
  }
  resolution = 3.48
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.73, per 1000 atoms: 0.21
  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: 1.18
  Conformation dependent library (CDL) restraints added in 470.8 milliseconds
  

  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: 1.91
  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: 2.00

  Time building geometry restraints manager: 1.62 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:             1.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.530
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.800
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (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
 ARG   0.003   0.000   ARG F  92 
 TYR   0.018   0.002   TYR F  88 
 PHE   0.009   0.001   PHE A  67 
 HIS   0.004   0.001   HIS C  31 

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

*********************** 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  : 0.299 
Fit side-chains
REVERT: G   61 GLU cc_start: 0.7469 (tp30) cc_final: 0.7258 (tp30)
REVERT: H   59 MET cc_start: 0.8586 (tpp) cc_final: 0.8375 (tpp)
REVERT: H  116 LYS cc_start: 0.7879 (ttpp) cc_final: 0.7607 (ttpp)
REVERT: E   58 THR cc_start: 0.8782 (p) cc_final: 0.8522 (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: -0.0747 (mmm160)
REVERT: K    1 MET cc_start: 0.0618 (tpt) cc_final: 0.0261 (tpt)
  outliers start: 2
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1130
  time to fit residues: 22.7577
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  : 0.242 
-------------------------------------------------------------------------------
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 108 optimal weight:   10.0000
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
G  73 ASN
G 110 ASN
D  63 ASN
C  38 ASN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.107968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.070470 restraints weight = 31730.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 2.99
r_work: 0.2847 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2845
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2838 r_free = 0.2838    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2838
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1254

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= 0.204
  Angle     :  0.606   6.517  20213  Z= 0.358
  Chirality :  0.038   0.177   2311
  Planarity :  0.004   0.044   1552
  Dihedral  : 30.436 172.429   4206
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  6.67 %
    Favored  : 91.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.29), residues: 895
  helix:  1.67 (0.23), residues: 571
  sheet: -0.96 (0.71), residues: 50
  loop : -0.01 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  74 
 TYR   0.017   0.002   TYR H  40 
 PHE   0.011   0.002   PHE F  61 
 HIS   0.004   0.001   HIS K  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 (14042)
  covalent geometry    : angle       0.60554 (20213)
  hydrogen bonds       : bond        0.04773 (  767)
  hydrogen bonds       : angle       3.52168 ( 1915)

*********************** 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
  143 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.315 
Fit side-chains
REVERT: F   25 ASN cc_start: 0.8441 (m-40) cc_final: 0.8201 (m-40)
REVERT: G   61 GLU cc_start: 0.8074 (tp30) cc_final: 0.7816 (tp30)
REVERT: D   40 TYR cc_start: 0.9053 (m-80) cc_final: 0.8841 (m-80)
REVERT: B   25 ASN cc_start: 0.8937 (m110) cc_final: 0.8590 (m-40)
  outliers start: 14
  outliers final: 11
  residues processed: 136
  average time/residue: 0.1175
  time to fit residues: 22.7687
Evaluate side-chains
  127 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
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 H residue   52 THR
Chi-restraints excluded: chain A residue   46 VAL
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 C residue   38 ASN
Chi-restraints excluded: chain B residue   26 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 107 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 112 optimal weight:   20.0000
   chunk 71 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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
B  25 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.106665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.069175 restraints weight = 32140.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 2.83
r_work: 0.2820 rms_B_bonded: 4.13 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 = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2817 r_free = 0.2817    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2817
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1687

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= 0.236
  Angle     :  0.625   6.883  20213  Z= 0.366
  Chirality :  0.039   0.187   2311
  Planarity :  0.004   0.045   1552
  Dihedral  : 30.721 172.150   4202
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  :  9.02 %
    Favored  : 88.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.29), residues: 895
  helix:  1.59 (0.22), residues: 571
  sheet: -0.60 (0.74), residues: 50
  loop : -0.18 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 131 
 TYR   0.018   0.002   TYR H  40 
 PHE   0.013   0.002   PHE F  61 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 (14042)
  covalent geometry    : angle       0.62525 (20213)
  hydrogen bonds       : bond        0.05060 (  767)
  hydrogen bonds       : angle       3.34985 ( 1915)

*********************** 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
  129 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.406 
Fit side-chains
REVERT: F   25 ASN cc_start: 0.8449 (m-40) cc_final: 0.8207 (m-40)
REVERT: F   88 TYR cc_start: 0.6617 (m-10) cc_final: 0.6324 (m-10)
REVERT: E   73 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8515 (pp20)
  outliers start: 18
  outliers final: 11
  residues processed: 120
  average time/residue: 0.1295
  time to fit residues: 21.9916
Evaluate side-chains
  113 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
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   52 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain A residue   46 VAL
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   60 VAL
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 0 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   chunk 98 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 53 optimal weight:    4.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
G  73 ASN
A 108 ASN
A 125 GLN
D  67 ASN
C  38 ASN
C  73 ASN
L  40 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.108560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.074963 restraints weight = 32070.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 2.27
r_work: 0.2857 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  14042  Z= 0.159
  Angle     :  0.558   6.126  20213  Z= 0.333
  Chirality :  0.036   0.159   2311
  Planarity :  0.004   0.045   1552
  Dihedral  : 30.385 171.825   4202
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 10.20 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.29), residues: 895
  helix:  1.93 (0.23), residues: 570
  sheet: -0.11 (0.73), residues: 50
  loop : -0.15 (0.38), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 131 
 TYR   0.018   0.001   TYR D  40 
 PHE   0.010   0.002   PHE A  67 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (14042)
  covalent geometry    : angle       0.55833 (20213)
  hydrogen bonds       : bond        0.04192 (  767)
  hydrogen bonds       : angle       3.09608 ( 1915)

*********************** 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
  147 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.284 
Fit side-chains
REVERT: E   76 GLN cc_start: 0.8039 (tp-100) cc_final: 0.7716 (pt0)
REVERT: D   59 MET cc_start: 0.8896 (tpp) cc_final: 0.8405 (tpp)
REVERT: B   25 ASN cc_start: 0.8859 (m-40) cc_final: 0.8196 (m-40)
  outliers start: 16
  outliers final: 10
  residues processed: 138
  average time/residue: 0.1179
  time to fit residues: 23.3257
Evaluate side-chains
  127 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
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 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   38 ASN
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain K residue    1 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 107 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 113 optimal weight:    5.9990
   chunk 98 optimal weight:    7.9990
   chunk 85 optimal weight:    8.9990
   chunk 38 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 63 optimal weight:    0.4980
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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  38 ASN
C  73 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.107789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.070570 restraints weight = 32255.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 2.78
r_work: 0.2857 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2852
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14042  Z= 0.184
  Angle     :  0.578   6.229  20213  Z= 0.342
  Chirality :  0.037   0.169   2311
  Planarity :  0.004   0.044   1552
  Dihedral  : 30.471 172.211   4202
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 11.11 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.29), residues: 895
  helix:  1.92 (0.22), residues: 571
  sheet: -0.04 (0.74), residues: 50
  loop : -0.22 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  86 
 TYR   0.022   0.002   TYR D  40 
 PHE   0.011   0.002   PHE A  67 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (14042)
  covalent geometry    : angle       0.57785 (20213)
  hydrogen bonds       : bond        0.04468 (  767)
  hydrogen bonds       : angle       3.12045 ( 1915)

*********************** 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
  140 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.339 
Fit side-chains
REVERT: F   25 ASN cc_start: 0.8522 (m-40) cc_final: 0.8221 (m-40)
REVERT: H   80 LEU cc_start: 0.9166 (tp) cc_final: 0.8958 (tp)
REVERT: E   73 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8475 (pp20)
REVERT: C  101 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8905 (p)
REVERT: B   25 ASN cc_start: 0.8847 (m-40) cc_final: 0.8201 (m-40)
  outliers start: 21
  outliers final: 14
  residues processed: 131
  average time/residue: 0.1072
  time to fit residues: 20.4261
Evaluate side-chains
  130 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
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   78 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  133 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   38 ASN
Chi-restraints excluded: chain C residue   96 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 27 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 98 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 78 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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  38 ASN
C  73 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.107775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.070565 restraints weight = 31846.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 2.85
r_work: 0.2861 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2858
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2858
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.1875

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= 0.177
  Angle     :  0.573   6.721  20213  Z= 0.339
  Chirality :  0.037   0.163   2311
  Planarity :  0.004   0.044   1552
  Dihedral  : 30.419 172.255   4202
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 11.63 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.29), residues: 895
  helix:  1.96 (0.23), residues: 569
  sheet:  0.05 (0.75), residues: 50
  loop : -0.27 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  33 
 TYR   0.024   0.002   TYR D  40 
 PHE   0.011   0.002   PHE A  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (14042)
  covalent geometry    : angle       0.57261 (20213)
  hydrogen bonds       : bond        0.04343 (  767)
  hydrogen bonds       : angle       3.09367 ( 1915)

*********************** 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: 21
    poor density    : 119
  time to evaluate  : 0.322 
Fit side-chains
REVERT: H   80 LEU cc_start: 0.9219 (tp) cc_final: 0.9009 (tp)
REVERT: E   73 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8474 (pp20)
REVERT: D   59 MET cc_start: 0.8918 (tpp) cc_final: 0.8378 (tpp)
REVERT: C  101 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8917 (p)
REVERT: B   25 ASN cc_start: 0.8845 (m-40) cc_final: 0.8233 (m-40)
  outliers start: 21
  outliers final: 14
  residues processed: 131
  average time/residue: 0.1166
  time to fit residues: 22.0247
Evaluate side-chains
  131 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
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   78 ILE
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  133 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   38 ASN
Chi-restraints excluded: chain C residue   96 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 108 optimal weight:    7.9990
   chunk 89 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0570
   chunk 6 optimal weight:    3.9990
   chunk 110 optimal weight:    0.4980
   chunk 40 optimal weight:    0.2980
   chunk 71 optimal weight:    0.9990
   chunk 104 optimal weight:   10.0000
   overall best weight:    0.5500

-------------------------------------------------------------------------------
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 125 GLN
D  84 ASN
C  38 ASN
C  73 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.109995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.073264 restraints weight = 31910.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 2.81
r_work: 0.2921 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2919
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2919 r_free = 0.2919    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2919 r_free = 0.2919    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2919
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.1944

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= 0.136
  Angle     :  0.538   7.099  20213  Z= 0.321
  Chirality :  0.035   0.142   2311
  Planarity :  0.003   0.045   1552
  Dihedral  : 30.127 171.904   4202
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.33 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.05 (0.29), residues: 895
  helix:  2.20 (0.23), residues: 568
  sheet:  0.31 (0.75), residues: 50
  loop : -0.18 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  79 
 TYR   0.022   0.001   TYR D  40 
 PHE   0.010   0.001   PHE E  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (14042)
  covalent geometry    : angle       0.53807 (20213)
  hydrogen bonds       : bond        0.03890 (  767)
  hydrogen bonds       : angle       2.96362 ( 1915)

*********************** 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
  145 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.260 
Fit side-chains
REVERT: H   80 LEU cc_start: 0.9172 (tp) cc_final: 0.8962 (tp)
REVERT: H   86 ARG cc_start: 0.7764 (mtt180) cc_final: 0.7349 (mtt-85)
REVERT: E   58 THR cc_start: 0.8891 (p) cc_final: 0.8644 (p)
REVERT: E   73 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8477 (pp20)
REVERT: E   76 GLN cc_start: 0.8051 (tp-100) cc_final: 0.7723 (pt0)
REVERT: E  129 ARG cc_start: 0.7793 (tmt170) cc_final: 0.7497 (tpt90)
REVERT: D   59 MET cc_start: 0.8879 (tpp) cc_final: 0.8184 (tpp)
REVERT: D   68 ASP cc_start: 0.8809 (t0) cc_final: 0.8547 (t0)
REVERT: C  101 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8924 (p)
REVERT: B   25 ASN cc_start: 0.8746 (m-40) cc_final: 0.8181 (m-40)
  outliers start: 14
  outliers final: 9
  residues processed: 138
  average time/residue: 0.1184
  time to fit residues: 23.1987
Evaluate side-chains
  136 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   91 LYS
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 C residue   38 ASN
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 65 optimal weight:    2.9990
   chunk 111 optimal weight:    9.9990
   chunk 82 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0770
   chunk 87 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   chunk 76 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9990
   chunk 64 optimal weight:    0.5980
   chunk 83 optimal weight:    5.9990
   overall best weight:    1.3344

-------------------------------------------------------------------------------
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  38 ASN
C  73 ASN
K  41 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.108496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.071488 restraints weight = 31762.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 3.00
r_work: 0.2876 rms_B_bonded: 4.18 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 = 0.57   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 = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2873
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14042  Z= 0.174
  Angle     :  0.570   7.221  20213  Z= 0.335
  Chirality :  0.036   0.169   2311
  Planarity :  0.004   0.045   1552
  Dihedral  : 30.328 172.506   4202
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 13.73 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.29), residues: 895
  helix:  2.14 (0.23), residues: 568
  sheet:  0.44 (0.76), residues: 50
  loop : -0.22 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  86 
 TYR   0.024   0.002   TYR D  40 
 PHE   0.010   0.002   PHE A  67 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (14042)
  covalent geometry    : angle       0.57005 (20213)
  hydrogen bonds       : bond        0.04328 (  767)
  hydrogen bonds       : angle       3.03304 ( 1915)

*********************** 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: 15
    poor density    : 121
  time to evaluate  : 0.252 
Fit side-chains
REVERT: H   80 LEU cc_start: 0.9225 (tp) cc_final: 0.9007 (tp)
REVERT: E   73 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8372 (pp20)
REVERT: E   76 GLN cc_start: 0.8075 (tp-100) cc_final: 0.7730 (pt0)
REVERT: A  129 ARG cc_start: 0.8531 (tpt90) cc_final: 0.7962 (tpt90)
REVERT: D   59 MET cc_start: 0.8861 (tpp) cc_final: 0.8221 (tpp)
REVERT: C  101 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8911 (p)
REVERT: B   25 ASN cc_start: 0.8838 (m-40) cc_final: 0.8248 (m-40)
REVERT: B   68 ASP cc_start: 0.8398 (m-30) cc_final: 0.8195 (m-30)
  outliers start: 15
  outliers final: 11
  residues processed: 131
  average time/residue: 0.1115
  time to fit residues: 21.0829
Evaluate side-chains
  130 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   91 LYS
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   52 THR
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue   96 LEU
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 31 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 87 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 96 optimal weight:    4.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 125 GLN
C  38 ASN
C  73 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.108733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.072903 restraints weight = 32013.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.99
r_work: 0.2871 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2871
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2871 r_free = 0.2871    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2871
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2057

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= 0.157
  Angle     :  0.559   8.074  20213  Z= 0.330
  Chirality :  0.036   0.156   2311
  Planarity :  0.004   0.045   1552
  Dihedral  : 30.262 172.329   4202
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 13.73 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.02 (0.29), residues: 895
  helix:  2.16 (0.23), residues: 568
  sheet:  0.60 (0.77), residues: 50
  loop : -0.21 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  33 
 TYR   0.027   0.002   TYR D  40 
 PHE   0.010   0.002   PHE E  67 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (14042)
  covalent geometry    : angle       0.55870 (20213)
  hydrogen bonds       : bond        0.04141 (  767)
  hydrogen bonds       : angle       2.99190 ( 1915)

*********************** 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
  143 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.357 
Fit side-chains
REVERT: H   35 GLU cc_start: 0.6200 (OUTLIER) cc_final: 0.5726 (tt0)
REVERT: H   80 LEU cc_start: 0.9228 (tp) cc_final: 0.9019 (tp)
REVERT: H   86 ARG cc_start: 0.7839 (mtt180) cc_final: 0.7382 (mtt180)
REVERT: E   58 THR cc_start: 0.8910 (p) cc_final: 0.8658 (p)
REVERT: E   73 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8403 (pp20)
REVERT: E   76 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7717 (pt0)
REVERT: A  129 ARG cc_start: 0.8524 (tpt90) cc_final: 0.8028 (tpt90)
REVERT: D   59 MET cc_start: 0.8842 (tpp) cc_final: 0.8261 (tpp)
REVERT: C  101 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8932 (p)
REVERT: B   25 ASN cc_start: 0.8816 (m-40) cc_final: 0.8316 (m-40)
REVERT: B   68 ASP cc_start: 0.8386 (m-30) cc_final: 0.8186 (m-30)
  outliers start: 20
  outliers final: 12
  residues processed: 135
  average time/residue: 0.1092
  time to fit residues: 21.3635
Evaluate side-chains
  134 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain H residue   35 GLU
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  133 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   38 ASN
Chi-restraints excluded: chain C residue   96 LEU
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 52 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 104 optimal weight:    8.9990
   chunk 103 optimal weight:    9.9990
   chunk 89 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 113 optimal weight:   20.0000
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    6.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.107967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.070945 restraints weight = 31982.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 2.96
r_work: 0.2868 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  14042  Z= 0.187
  Angle     :  0.586   8.039  20213  Z= 0.343
  Chirality :  0.037   0.171   2311
  Planarity :  0.004   0.045   1552
  Dihedral  : 30.387 172.533   4202
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 14.25 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.93 (0.29), residues: 895
  helix:  2.07 (0.23), residues: 568
  sheet:  0.66 (0.78), residues: 50
  loop : -0.24 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  79 
 TYR   0.027   0.002   TYR D  40 
 PHE   0.010   0.002   PHE F  61 
 HIS   0.007   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (14042)
  covalent geometry    : angle       0.58617 (20213)
  hydrogen bonds       : bond        0.04424 (  767)
  hydrogen bonds       : angle       3.04320 ( 1915)

********************** 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
  132 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.353 
Fit side-chains
REVERT: H   35 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.5651 (tt0)
REVERT: H   86 ARG cc_start: 0.7844 (mtt180) cc_final: 0.7512 (mtt180)
REVERT: E   73 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8368 (pp20)
REVERT: E   76 GLN cc_start: 0.8073 (tp-100) cc_final: 0.7714 (pt0)
REVERT: D   59 MET cc_start: 0.8863 (tpp) cc_final: 0.8317 (tpp)
REVERT: C  101 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8911 (p)
REVERT: B   25 ASN cc_start: 0.8830 (m-40) cc_final: 0.8349 (m-40)
REVERT: B   68 ASP cc_start: 0.8403 (m-30) cc_final: 0.8190 (m-30)
  outliers start: 16
  outliers final: 12
  residues processed: 125
  average time/residue: 0.1157
  time to fit residues: 20.8417
Evaluate side-chains
  130 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   91 LYS
Chi-restraints excluded: chain H residue   35 GLU
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  133 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   62 ILE
Chi-restraints excluded: chain C residue   96 LEU
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 25 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0670
   chunk 71 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   chunk 93 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 87 optimal weight:    6.9990
   chunk 105 optimal weight:    0.0050
   overall best weight:    0.5334

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.109048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.072270 restraints weight = 31704.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 3.01
r_work: 0.2894 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2893
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2893 r_free = 0.2893    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2893 r_free = 0.2893    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2893
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.2108

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= 0.136
  Angle     :  0.555   8.615  20213  Z= 0.329
  Chirality :  0.036   0.147   2311
  Planarity :  0.003   0.045   1552
  Dihedral  : 30.308 172.450   4202
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.64 %
    Favored  : 83.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.10 (0.29), residues: 895
  helix:  2.18 (0.23), residues: 568
  sheet:  0.81 (0.78), residues: 50
  loop : -0.12 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  29 
 TYR   0.027   0.002   TYR D  40 
 PHE   0.010   0.001   PHE E  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (14042)
  covalent geometry    : angle       0.55547 (20213)
  hydrogen bonds       : bond        0.04048 (  767)
  hydrogen bonds       : angle       2.97255 ( 1915)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3123.11 seconds
wall clock time: 53 minutes 48.00 seconds (3228.00 seconds total)