Starting phenix.real_space_refine
on Wed Sep 17 03:37:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ve5_43165/09_2025/8ve5_43165.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ve5_43165/09_2025/8ve5_43165.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ve5_43165/09_2025/8ve5_43165.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ve5_43165/09_2025/8ve5_43165.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ve5_43165/09_2025/8ve5_43165.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ve5_43165/09_2025/8ve5_43165.map"
  }
  resolution = 3.4
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S       3      5.16       5
     Cl      2      4.86       5
     C    2201      2.51       5
     N     576      2.21       5
     O     600      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3382
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 860
          Classifications: {'peptide': 117}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 7, 'TRANS': 109}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 27
    Chain: "B"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 837
          Classifications: {'peptide': 117}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 7, 'TRANS': 109}
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 86
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 7, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 45
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 827
          Classifications: {'peptide': 116}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 7, 'TRANS': 108}
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 89
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 44
    Chain: "D"
      Number of atoms: 839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 839
          Classifications: {'peptide': 117}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 7, 'TRANS': 109}
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 83
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 38
    Chain: "B"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Unusual residues: {'P2C': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
  Time building chain proxies: 1.07, per 1000 atoms: 0.32
  Number of scatterers: 3382
  At special positions: 0
  Unit cell: (76.994, 67.44, 60.696, 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)
     Cl      2     17.00
     S       3     16.00
     O     600      8.00
     N     576      7.00
     C    2201      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: 0.17
  Conformation dependent library (CDL) restraints added in 117.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  878

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 5 sheets defined
      7.1% alpha, 51.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 75 through 82
      removed outlier: 3.788A  pdb=" N   LEU A  82 " --> pdb=" O   TYR A  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 83
      removed outlier: 3.751A  pdb=" N   LEU B  82 " --> pdb=" O   TYR B  78 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 75 through 82
      removed outlier: 3.674A  pdb=" N   TRP C  79 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LYS C  80 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 75 through 82
      removed outlier: 3.635A  pdb=" N   LYS D  80 " --> pdb=" O   LYS D  76 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU D  82 " --> pdb=" O   TYR D  78 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55
      removed outlier: 3.649A  pdb=" N   VAL A  14 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   MET A  13 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   ALA A 109 " --> pdb=" O   MET A  13 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   LYS A  15 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   LEU A 111 " --> pdb=" O   LYS A  15 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LEU A  17 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
      removed outlier: 5.772A  pdb=" N   MET B  13 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   ALA B 109 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   LYS B  15 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   LEU B 111 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   LEU B  17 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55
      removed outlier: 3.649A  pdb=" N   VAL A  14 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   MET A  13 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   ALA A 109 " --> pdb=" O   MET A  13 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   LYS A  15 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   LEU A 111 " --> pdb=" O   LYS A  15 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LEU A  17 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
      removed outlier: 5.772A  pdb=" N   MET B  13 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   ALA B 109 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   LYS B  15 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   LEU B 111 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   LEU B  17 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 48
      removed outlier: 5.470A  pdb=" N   ARG A  34 " --> pdb=" O   PRO A  43 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ALA A  29 " --> pdb=" O   ASP A  74 " (cutoff:3.500A)
      removed outlier: 5.046A  pdb=" N   ILE A  68 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   VAL B  94 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   ALA A  91 " --> pdb=" O   GLU B  92 " (cutoff:3.500A)
      removed outlier: 9.337A  pdb=" N   GLU B  92 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   VAL A  93 " --> pdb=" O   HIS B  90 " (cutoff:3.500A)
      removed outlier: 8.245A  pdb=" N   HIS B  90 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   PHE A  95 " --> pdb=" O   HIS B  88 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   HIS B  88 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLY B  67 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 5.113A  pdb=" N   ILE B  68 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   ARG B  34 " --> pdb=" O   PRO B  43 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 12 through 18
      removed outlier: 6.007A  pdb=" N   MET C  13 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 7.352A  pdb=" N   ALA C 109 " --> pdb=" O   MET C  13 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   LYS C  15 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   LEU C 111 " --> pdb=" O   LYS C  15 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   LEU C  17 " --> pdb=" O   LEU C 111 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   THR C 119 " --> pdb=" O   ALA C 108 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU C 110 " --> pdb=" O   SER C 117 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   THR D 119 " --> pdb=" O   ALA D 108 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   MET D  13 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   ALA D 109 " --> pdb=" O   MET D  13 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   LYS D  15 " --> pdb=" O   ALA D 109 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   LEU D 111 " --> pdb=" O   LYS D  15 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   LEU D  17 " --> pdb=" O   LEU D 111 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   VAL D  14 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 41 through 48
      removed outlier: 6.473A  pdb=" N   VAL C  32 " --> pdb=" O   PHE C  44 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   SER C  46 " --> pdb=" O   VAL C  30 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   VAL C  30 " --> pdb=" O   SER C  46 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ALA C  29 " --> pdb=" O   ASP C  74 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LYS C  70 " --> pdb=" O   PHE C  33 " (cutoff:3.500A)
      removed outlier: 5.262A  pdb=" N   ILE C  68 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   PHE C  95 " --> pdb=" O   TYR C  69 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   HIS C  88 " --> pdb=" O   PHE D  95 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   PHE D  95 " --> pdb=" O   HIS C  88 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   HIS C  90 " --> pdb=" O   VAL D  93 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   VAL D  93 " --> pdb=" O   HIS C  90 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   GLU C  92 " --> pdb=" O   ALA D  91 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   ALA D  91 " --> pdb=" O   GLU C  92 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   VAL C  94 " --> pdb=" O   GLU D  89 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLY D  67 " --> pdb=" O   ALA D  97 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   ILE D  68 " --> pdb=" O   LYS D  35 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   VAL D  30 " --> pdb=" O   SER D  46 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   SER D  46 " --> pdb=" O   VAL D  30 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   VAL D  32 " --> pdb=" O   PHE D  44 " (cutoff:3.500A)

    141 hydrogen bonds defined for protein.
    396 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.40

  Time building geometry restraints manager: 0.24 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1070
        1.34 -     1.46: 853
        1.46 -     1.57: 1547
        1.57 -     1.69: 1
        1.69 -     1.81: 7
  Bond restraints: 3478
  Sorted by residual:
  bond pdb=" CB  PRO C 125 "
       pdb=" CG  PRO C 125 "
    ideal  model  delta    sigma   weight residual
    1.492  1.608 -0.116 5.00e-02 4.00e+02 5.40e+00
  bond pdb=" C5  P2C B 201 "
       pdb=" N18 P2C B 201 "
    ideal  model  delta    sigma   weight residual
    1.361  1.402 -0.041 2.00e-02 2.50e+03 4.25e+00
  bond pdb=" C13 P2C B 201 "
       pdb=" C19 P2C B 201 "
    ideal  model  delta    sigma   weight residual
    1.527  1.497  0.030 2.00e-02 2.50e+03 2.20e+00
  bond pdb=" CB  VAL D  16 "
       pdb=" CG1 VAL D  16 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.36e-01
  bond pdb=" N   PRO C 125 "
       pdb=" CA  PRO C 125 "
    ideal  model  delta    sigma   weight residual
    1.466  1.453  0.013 1.50e-02 4.44e+03 7.39e-01
  ... (remaining 3473 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 4656
        1.61 -     3.22: 98
        3.22 -     4.83: 15
        4.83 -     6.44: 2
        6.44 -     8.05: 1
  Bond angle restraints: 4772
  Sorted by residual:
  angle pdb=" CA  PRO C 125 "
        pdb=" N   PRO C 125 "
        pdb=" CD  PRO C 125 "
      ideal   model   delta    sigma   weight residual
     112.00  105.60    6.40 1.40e+00 5.10e-01 2.09e+01
  angle pdb=" N   PRO C 125 "
        pdb=" CD  PRO C 125 "
        pdb=" CG  PRO C 125 "
      ideal   model   delta    sigma   weight residual
     103.20   99.21    3.99 1.50e+00 4.44e-01 7.07e+00
  angle pdb=" CA  LYS C  15 "
        pdb=" CB  LYS C  15 "
        pdb=" CG  LYS C  15 "
      ideal   model   delta    sigma   weight residual
     114.10  118.75   -4.65 2.00e+00 2.50e-01 5.40e+00
  angle pdb=" N   PHE A  44 "
        pdb=" CA  PHE A  44 "
        pdb=" C   PHE A  44 "
      ideal   model   delta    sigma   weight residual
     113.18  110.11    3.07 1.33e+00 5.65e-01 5.32e+00
  angle pdb=" CB  LYS D  15 "
        pdb=" CG  LYS D  15 "
        pdb=" CD  LYS D  15 "
      ideal   model   delta    sigma   weight residual
     111.30  106.49    4.81 2.30e+00 1.89e-01 4.38e+00
  ... (remaining 4767 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.04: 1866
       16.04 -    32.08: 108
       32.08 -    48.12: 23
       48.12 -    64.16: 4
       64.16 -    80.20: 3
  Dihedral angle restraints: 2004
    sinusoidal: 644
      harmonic: 1360
  Sorted by residual:
  dihedral pdb=" CA  PRO B  86 "
           pdb=" C   PRO B  86 "
           pdb=" N   PHE B  87 "
           pdb=" CA  PHE B  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.67   17.33     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  SER A  23 "
           pdb=" C   SER A  23 "
           pdb=" N   PRO A  24 "
           pdb=" CA  PRO A  24 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.84   17.16     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CB  GLU A  72 "
           pdb=" CG  GLU A  72 "
           pdb=" CD  GLU A  72 "
           pdb=" OE1 GLU A  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -80.20   80.20     1      3.00e+01 1.11e-03 8.85e+00
  ... (remaining 2001 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 282
       0.027 -    0.053: 156
       0.053 -    0.079: 42
       0.079 -    0.106: 42
       0.106 -    0.132: 32
  Chirality restraints: 554
  Sorted by residual:
  chirality pdb=" CA  ILE B  73 "
            pdb=" N   ILE B  73 "
            pdb=" C   ILE B  73 "
            pdb=" CB  ILE B  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.38e-01
  chirality pdb=" CA  ILE B  84 "
            pdb=" N   ILE B  84 "
            pdb=" C   ILE B  84 "
            pdb=" CB  ILE B  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.20e-01
  chirality pdb=" CA  ILE C  73 "
            pdb=" N   ILE C  73 "
            pdb=" C   ILE C  73 "
            pdb=" CB  ILE C  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.19e-01
  ... (remaining 551 not shown)

  Planarity restraints: 605
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 101 "   -0.036 5.00e-02 4.00e+02   5.50e-02 4.84e+00
        pdb=" N   PRO A 102 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 102 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 102 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  85 "   -0.030 5.00e-02 4.00e+02   4.55e-02 3.31e+00
        pdb=" N   PRO B  86 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B  86 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B  86 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  23 "    0.021 5.00e-02 4.00e+02   3.15e-02 1.59e+00
        pdb=" N   PRO B  24 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B  24 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B  24 "    0.018 5.00e-02 4.00e+02
  ... (remaining 602 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 418
        2.75 -     3.29: 3069
        3.29 -     3.83: 5484
        3.83 -     4.36: 6079
        4.36 -     4.90: 11549
  Nonbonded interactions: 26599
  Sorted by model distance:
  nonbonded pdb=" O   VAL B  65 "
            pdb=" OH  TYR B  69 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OD2 ASP B  18 "
            pdb=" NH2 ARG B  21 "
     model   vdw
     2.327 3.120
  nonbonded pdb=" OD2 ASP B  18 "
            pdb=" OH  TYR B  78 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" O   PHE B  64 "
            pdb=" ND2 ASN B  98 "
     model   vdw
     2.332 3.120
  nonbonded pdb=" O   THR C  60 "
            pdb=" N   PHE C  64 "
     model   vdw
     2.374 3.120
  ... (remaining 26594 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 10 through 12 or (resid 13 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 14 through 22 or (resid 23 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 24 through 25 or (resid 26 throu \ 
gh 27 and (name N or name CA or name C or name O or name CB )) or resid 28 throu \ 
gh 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 43 through 48 or (resid 49 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 50 or (resid 51 through 52 and (name N or name CA or name C or \ 
 name O or name CB )) or (resid 53 through 56 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 57 through 58 or (resid 59 through 63 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 64 or (resid 65 through  \ 
66 and (name N or name CA or name C or name O or name CB )) or resid 67 through  \ 
68 or (resid 69 and (name N or name CA or name C or name O or name CB or name CG \ 
 or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 70 throu \ 
gh 73 or (resid 74 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 75 or (resid 76 through 77 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 78 through 79 or (resid 80 through 81 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 82 through 84 or (resid 85 and (name N \ 
 or name CA or name C or name O or name CB )) or resid 86 through 88 or (resid 8 \ 
9 and (name N or name CA or name C or name O or name CB )) or resid 90 through 9 \ 
1 or (resid 92 and (name N or name CA or name C or name O or name CB )) or resid \ 
 93 through 98 or (resid 99 through 100 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 101 through 102 or (resid 103 through 104 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 105 or (resid 106 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 107 through 111 or (re \ 
sid 112 and (name N or name CA or name C or name O or name CB )) or resid 113 th \ 
rough 114 or (resid 115 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 116 or (resid 117 and (name N or name CA or name C or name O or name C \ 
B )) or resid 118 or (resid 119 through 120 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 121 through 122 or (resid 123 through 124 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 125))
  selection = (chain 'B' and ((resid 10 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 11 through 14 or (resid 15 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 16 through 22 or (resid 23 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 24 through 25 or (resid 26 through 27 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 28 through 33 or ( \ 
resid 34 and (name N or name CA or name C or name O or name CB )) or resid 35 th \ 
rough 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) o \ 
r resid 47 or (resid 48 through 49 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 50 through 51 or (resid 52 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 53 or (resid 54 through 56 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 57 through 58 or (resid 59 throug \ 
h 63 and (name N or name CA or name C or name O or name CB )) or resid 64 throug \ 
h 68 or (resid 69 and (name N or name CA or name C or name O or name CB or name  \ 
CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 70 thr \ 
ough 76 or (resid 77 and (name N or name CA or name C or name O or name CB )) or \ 
 resid 78 through 84 or (resid 85 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 86 through 102 or (resid 103 through 104 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 105 or (resid 106 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 107 through 116 or (resid 117 \ 
 and (name N or name CA or name C or name O or name CB )) or resid 118 or (resid \ 
 119 through 120 and (name N or name CA or name C or name O or name CB )) or res \ 
id 121 through 123 or (resid 124 and (name N or name CA or name C or name O or n \ 
ame CB )) or resid 125))
  selection = (chain 'C' and (resid 10 through 12 or (resid 13 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 14 or (resid 15 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 16 through 22 or (resid 23 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 24 through 25 or (resid 26 thr \ 
ough 27 and (name N or name CA or name C or name O or name CB )) or resid 28 thr \ 
ough 33 or (resid 34 and (name N or name CA or name C or name O or name CB )) or \ 
 resid 35 through 41 or (resid 42 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 43 through 47 or (resid 48 through 49 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 50 through 54 or (resid 55 through 5 \ 
6 and (name N or name CA or name C or name O or name CB )) or resid 57 through 6 \ 
0 or (resid 61 through 63 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 64 through 68 or (resid 69 and (name N or name CA or name C or name  \ 
O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name  \ 
CZ )) or resid 70 through 75 or (resid 76 through 77 and (name N or name CA or n \ 
ame C or name O or name CB )) or resid 78 through 79 or (resid 80 through 81 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 82 through 88 or  \ 
(resid 89 and (name N or name CA or name C or name O or name CB )) or resid 90 t \ 
hrough 98 or (resid 99 through 100 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 101 through 103 or (resid 104 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 105 through 125))
  selection = (chain 'D' and (resid 10 through 14 or (resid 15 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 16 through 33 or (resid 34 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 35 through 37 or (resid 38 throu \ 
gh 40 and (name N or name CA or name C or name O or name CB )) or resid 41 throu \ 
gh 47 or (resid 48 through 49 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 50 or (resid 51 through 52 and (name N or name CA or name C or n \ 
ame O or name CB )) or resid 53 or (resid 54 through 56 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 57 through 58 or (resid 59 through 63  \ 
and (name N or name CA or name C or name O or name CB )) or resid 64 through 75  \ 
or (resid 76 through 77 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 78 through 79 or (resid 80 through 81 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 82 through 84 or (resid 85 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 86 through 102 or (resid 103 thro \ 
ugh 104 and (name N or name CA or name C or name O or name CB )) or resid 105 or \ 
 (resid 106 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 
7 through 111 or (resid 112 and (name N or name CA or name C or name O or name C \ 
B )) or resid 113 through 114 or (resid 115 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 116 or (resid 117 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 118 through 125))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     4.550
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
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      :  0.005   0.116   3478  Z= 0.189
  Angle     :  0.584   8.050   4772  Z= 0.309
  Chirality :  0.048   0.132    554
  Planarity :  0.005   0.055    605
  Dihedral  : 11.514  80.199   1126
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.41), residues: 459
  helix: -0.84 (0.87), residues: 28
  sheet:  0.80 (0.38), residues: 229
  loop :  0.26 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  34 
 TYR   0.013   0.002   TYR A  69 
 PHE   0.019   0.002   PHE B  44 
 TRP   0.011   0.002   TRP A  79 
 HIS   0.002   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 3478)
  covalent geometry    : angle       0.58405 ( 4772)
  hydrogen bonds       : bond        0.24484 (  120)
  hydrogen bonds       : angle      10.11676 (  396)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.5984 (ttp) cc_final: 0.5585 (tmm)
REVERT: A   14 VAL cc_start: 0.8843 (t) cc_final: 0.8503 (p)
REVERT: A  103 ARG cc_start: 0.7416 (mpt180) cc_final: 0.6898 (mmt-90)
REVERT: A  117 SER cc_start: 0.9277 (t) cc_final: 0.9075 (t)
REVERT: C   13 MET cc_start: 0.6619 (tmm) cc_final: 0.6302 (ptm)
REVERT: C   35 LYS cc_start: 0.7756 (tptt) cc_final: 0.7145 (tppt)
REVERT: D  103 ARG cc_start: 0.7710 (mmm160) cc_final: 0.7058 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.0877
  time to fit residues: 8.0018
Evaluate side-chains
  66 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0770
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.2980
   chunk 32 optimal weight:    0.0170
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0980
   chunk 22 optimal weight:    0.3980
   chunk 37 optimal weight:    5.9990
   overall best weight:    0.1776

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.161849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.125790 restraints weight = 4656.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 3.56
r_work: 0.3507 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.065   3478  Z= 0.098
  Angle     :  0.529   7.195   4772  Z= 0.277
  Chirality :  0.048   0.144    554
  Planarity :  0.005   0.045    605
  Dihedral  :  3.823  20.534    498
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  8.91 %
    Favored  : 89.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.41), residues: 459
  helix: -0.94 (0.80), residues: 28
  sheet:  1.36 (0.38), residues: 228
  loop : -0.04 (0.43), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  34 
 TYR   0.010   0.001   TYR D 116 
 PHE   0.007   0.001   PHE A  33 
 TRP   0.007   0.001   TRP C  79 
 HIS   0.001   0.000   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 3478)
  covalent geometry    : angle       0.52853 ( 4772)
  hydrogen bonds       : bond        0.03164 (  120)
  hydrogen bonds       : angle       6.86282 (  396)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.6141 (ttp) cc_final: 0.5402 (tmm)
REVERT: A   14 VAL cc_start: 0.9049 (t) cc_final: 0.8710 (p)
REVERT: A   80 LYS cc_start: 0.8200 (mmtm) cc_final: 0.7999 (mmtm)
REVERT: A  103 ARG cc_start: 0.7455 (mpt180) cc_final: 0.6644 (mmt-90)
REVERT: B   84 ILE cc_start: 0.7741 (mt) cc_final: 0.7484 (tt)
REVERT: C   13 MET cc_start: 0.6551 (tmm) cc_final: 0.6279 (ptm)
REVERT: D   34 ARG cc_start: 0.7798 (ttt180) cc_final: 0.7422 (ttt180)
REVERT: D   44 PHE cc_start: 0.8833 (t80) cc_final: 0.8592 (t80)
  outliers start: 5
  outliers final: 2
  residues processed: 86
  average time/residue: 0.0963
  time to fit residues: 9.6050
Evaluate side-chains
  78 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain B residue  110 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 1 optimal weight:    8.9990
   chunk 2 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 37 optimal weight:    0.7980
   chunk 25 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 36 optimal weight:    0.1980
   chunk 39 optimal weight:    7.9990
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.153828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.118017 restraints weight = 4700.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 3.54
r_work: 0.3406 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   3478  Z= 0.198
  Angle     :  0.577   6.723   4772  Z= 0.304
  Chirality :  0.050   0.147    554
  Planarity :  0.005   0.043    605
  Dihedral  :  4.127  19.104    498
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  :  8.91 %
    Favored  : 87.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.41), residues: 459
  helix: -1.44 (0.76), residues: 34
  sheet:  1.04 (0.37), residues: 229
  loop : -0.02 (0.45), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  34 
 TYR   0.013   0.001   TYR D 116 
 PHE   0.013   0.002   PHE D  44 
 TRP   0.009   0.002   TRP D  79 
 HIS   0.003   0.001   HIS C  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 3478)
  covalent geometry    : angle       0.57668 ( 4772)
  hydrogen bonds       : bond        0.03608 (  120)
  hydrogen bonds       : angle       6.71141 (  396)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.6289 (ttp) cc_final: 0.5737 (tmm)
REVERT: A   14 VAL cc_start: 0.9040 (t) cc_final: 0.8617 (m)
REVERT: C   13 MET cc_start: 0.6423 (tmm) cc_final: 0.6147 (ptm)
REVERT: D   34 ARG cc_start: 0.7891 (ttt180) cc_final: 0.7644 (ttt180)
REVERT: D   44 PHE cc_start: 0.8896 (t80) cc_final: 0.8671 (t80)
  outliers start: 12
  outliers final: 7
  residues processed: 73
  average time/residue: 0.0976
  time to fit residues: 8.1416
Evaluate side-chains
  73 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain D residue   59 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 36 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN
D  98 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.154869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.118684 restraints weight = 4647.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 3.59
r_work: 0.3418 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3478  Z= 0.152
  Angle     :  0.544   6.604   4772  Z= 0.284
  Chirality :  0.048   0.147    554
  Planarity :  0.005   0.039    605
  Dihedral  :  3.995  18.644    498
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  :  9.57 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.41), residues: 459
  helix: -1.43 (0.77), residues: 34
  sheet:  0.92 (0.37), residues: 229
  loop : -0.08 (0.44), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  34 
 TYR   0.014   0.001   TYR C 105 
 PHE   0.009   0.001   PHE D  44 
 TRP   0.007   0.001   TRP C  79 
 HIS   0.002   0.001   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 3478)
  covalent geometry    : angle       0.54367 ( 4772)
  hydrogen bonds       : bond        0.02987 (  120)
  hydrogen bonds       : angle       6.42144 (  396)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.6296 (ttp) cc_final: 0.5561 (tmm)
REVERT: A   14 VAL cc_start: 0.9022 (t) cc_final: 0.8638 (p)
REVERT: A  103 ARG cc_start: 0.7315 (mpt180) cc_final: 0.6593 (mmt-90)
REVERT: C   13 MET cc_start: 0.6407 (tmm) cc_final: 0.6114 (ptm)
REVERT: D   34 ARG cc_start: 0.7892 (ttt180) cc_final: 0.7674 (ttt180)
REVERT: D   44 PHE cc_start: 0.8875 (t80) cc_final: 0.8620 (t80)
  outliers start: 11
  outliers final: 10
  residues processed: 72
  average time/residue: 0.0874
  time to fit residues: 7.2895
Evaluate side-chains
  77 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue  115 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN
D  98 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.153032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.116978 restraints weight = 4712.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 3.56
r_work: 0.3393 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3478  Z= 0.191
  Angle     :  0.567   6.992   4772  Z= 0.297
  Chirality :  0.049   0.150    554
  Planarity :  0.005   0.038    605
  Dihedral  :  4.150  18.154    498
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 12.21 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.41), residues: 459
  helix: -1.37 (0.79), residues: 34
  sheet:  0.74 (0.37), residues: 229
  loop : -0.05 (0.45), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  34 
 TYR   0.015   0.002   TYR C 105 
 PHE   0.011   0.002   PHE D  44 
 TRP   0.008   0.001   TRP C  79 
 HIS   0.002   0.001   HIS C  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 3478)
  covalent geometry    : angle       0.56662 ( 4772)
  hydrogen bonds       : bond        0.03081 (  120)
  hydrogen bonds       : angle       6.43988 (  396)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.6392 (ttp) cc_final: 0.5821 (tmm)
REVERT: A   14 VAL cc_start: 0.9066 (t) cc_final: 0.8651 (m)
REVERT: A  103 ARG cc_start: 0.7311 (mpt180) cc_final: 0.6841 (mmt-90)
REVERT: C   13 MET cc_start: 0.6401 (tmm) cc_final: 0.6107 (ptm)
REVERT: D   44 PHE cc_start: 0.8898 (t80) cc_final: 0.8641 (t80)
  outliers start: 13
  outliers final: 10
  residues processed: 71
  average time/residue: 0.1093
  time to fit residues: 8.8140
Evaluate side-chains
  75 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue   84 ILE
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue  115 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0040
   chunk 38 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 14 optimal weight:    9.9990
   chunk 29 optimal weight:    0.0170
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.4632

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN
D  98 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.160955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.124783 restraints weight = 4636.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 3.59
r_work: 0.3499 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   3478  Z= 0.089
  Angle     :  0.500   6.735   4772  Z= 0.259
  Chirality :  0.047   0.134    554
  Planarity :  0.005   0.044    605
  Dihedral  :  3.696  19.648    498
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 14.52 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.40), residues: 459
  helix: -1.56 (0.74), residues: 34
  sheet:  0.99 (0.38), residues: 223
  loop : -0.24 (0.42), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  34 
 TYR   0.017   0.001   TYR C 105 
 PHE   0.007   0.001   PHE D  87 
 TRP   0.011   0.001   TRP C  79 
 HIS   0.001   0.000   HIS B  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 ( 3478)
  covalent geometry    : angle       0.50037 ( 4772)
  hydrogen bonds       : bond        0.02401 (  120)
  hydrogen bonds       : angle       5.78418 (  396)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.6354 (ttp) cc_final: 0.5706 (tmm)
REVERT: A  103 ARG cc_start: 0.7222 (mpt180) cc_final: 0.6478 (mmt-90)
REVERT: B   54 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.5989 (tm-30)
REVERT: C   13 MET cc_start: 0.6550 (tmm) cc_final: 0.6171 (ptm)
REVERT: C   15 LYS cc_start: 0.8020 (tmtt) cc_final: 0.7530 (tmtt)
REVERT: D   44 PHE cc_start: 0.8832 (t80) cc_final: 0.8557 (t80)
REVERT: D  105 TYR cc_start: 0.8464 (m-80) cc_final: 0.8111 (m-10)
  outliers start: 9
  outliers final: 6
  residues processed: 82
  average time/residue: 0.0985
  time to fit residues: 9.3639
Evaluate side-chains
  75 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   54 GLU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue  115 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 3 optimal weight:    8.9990
   chunk 41 optimal weight:    0.5980
   chunk 36 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 34 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 4 optimal weight:   10.0000
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN
D  98 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.155801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.119732 restraints weight = 4785.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3580 rms_B_bonded: 3.61
r_work: 0.3428 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3478  Z= 0.149
  Angle     :  0.549   6.611   4772  Z= 0.288
  Chirality :  0.048   0.144    554
  Planarity :  0.005   0.043    605
  Dihedral  :  3.853  18.850    498
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.83 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.41), residues: 459
  helix: -1.39 (0.80), residues: 34
  sheet:  1.04 (0.38), residues: 220
  loop : -0.33 (0.43), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  34 
 TYR   0.016   0.001   TYR C 105 
 PHE   0.009   0.001   PHE D  44 
 TRP   0.008   0.001   TRP C  79 
 HIS   0.002   0.001   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 3478)
  covalent geometry    : angle       0.54853 ( 4772)
  hydrogen bonds       : bond        0.02713 (  120)
  hydrogen bonds       : angle       5.95892 (  396)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.6394 (ttp) cc_final: 0.5789 (tmm)
REVERT: A  103 ARG cc_start: 0.7273 (mpt180) cc_final: 0.6480 (mmt-90)
REVERT: B   54 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.5972 (tm-30)
REVERT: C   13 MET cc_start: 0.6534 (tmm) cc_final: 0.6187 (ptm)
REVERT: C   15 LYS cc_start: 0.8049 (tmtt) cc_final: 0.7537 (tmtt)
REVERT: D   44 PHE cc_start: 0.8859 (t80) cc_final: 0.8559 (t80)
  outliers start: 8
  outliers final: 7
  residues processed: 70
  average time/residue: 0.0878
  time to fit residues: 7.2733
Evaluate side-chains
  73 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   54 GLU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue  115 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 37 optimal weight:    8.9990
   chunk 1 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN
D  98 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.151096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.115373 restraints weight = 4841.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 3.58
r_work: 0.3362 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   3478  Z= 0.235
  Angle     :  0.618   7.452   4772  Z= 0.325
  Chirality :  0.050   0.152    554
  Planarity :  0.006   0.040    605
  Dihedral  :  4.312  17.679    498
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 15.84 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.41), residues: 459
  helix: -1.39 (0.80), residues: 34
  sheet:  0.70 (0.37), residues: 226
  loop : -0.33 (0.45), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  34 
 TYR   0.018   0.002   TYR C 105 
 PHE   0.013   0.002   PHE D  44 
 TRP   0.011   0.001   TRP C  79 
 HIS   0.003   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 ( 3478)
  covalent geometry    : angle       0.61754 ( 4772)
  hydrogen bonds       : bond        0.03227 (  120)
  hydrogen bonds       : angle       6.41475 (  396)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.6432 (ttp) cc_final: 0.5840 (tmm)
REVERT: A   14 VAL cc_start: 0.9032 (t) cc_final: 0.8648 (m)
REVERT: A  103 ARG cc_start: 0.7274 (mpt180) cc_final: 0.6472 (mmt-90)
REVERT: B   78 TYR cc_start: 0.7845 (t80) cc_final: 0.7550 (t80)
REVERT: C   13 MET cc_start: 0.6408 (tmm) cc_final: 0.6093 (ptm)
REVERT: C   15 LYS cc_start: 0.8131 (tmtt) cc_final: 0.7637 (tmtt)
REVERT: C   35 LYS cc_start: 0.7786 (tptm) cc_final: 0.7463 (tptp)
REVERT: C   64 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6646 (m-80)
REVERT: D   44 PHE cc_start: 0.8902 (t80) cc_final: 0.8652 (t80)
REVERT: D  105 TYR cc_start: 0.8622 (m-80) cc_final: 0.8192 (m-10)
  outliers start: 11
  outliers final: 9
  residues processed: 70
  average time/residue: 0.0971
  time to fit residues: 7.8817
Evaluate side-chains
  74 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain C residue   64 PHE
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue  115 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 16 optimal weight:   20.0000
   chunk 39 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 26 optimal weight:    0.2980
   chunk 9 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0170
   overall best weight:    0.6020

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN
D  98 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.158778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.123167 restraints weight = 4651.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 3.55
r_work: 0.3468 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   3478  Z= 0.097
  Angle     :  0.525   6.606   4772  Z= 0.273
  Chirality :  0.048   0.140    554
  Planarity :  0.005   0.047    605
  Dihedral  :  3.819  18.816    498
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.50 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.41), residues: 459
  helix: -1.40 (0.81), residues: 34
  sheet:  0.81 (0.38), residues: 223
  loop : -0.30 (0.43), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  34 
 TYR   0.018   0.001   TYR C 105 
 PHE   0.007   0.001   PHE D  87 
 TRP   0.016   0.001   TRP C  79 
 HIS   0.002   0.001   HIS B  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 3478)
  covalent geometry    : angle       0.52505 ( 4772)
  hydrogen bonds       : bond        0.02369 (  120)
  hydrogen bonds       : angle       5.74703 (  396)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.6396 (ttp) cc_final: 0.5830 (tmm)
REVERT: A   14 VAL cc_start: 0.9023 (t) cc_final: 0.8609 (m)
REVERT: A  103 ARG cc_start: 0.7192 (mpt180) cc_final: 0.6428 (mmt-90)
REVERT: C   15 LYS cc_start: 0.8047 (tmtt) cc_final: 0.7599 (tmtt)
REVERT: C   35 LYS cc_start: 0.7765 (tptm) cc_final: 0.7369 (tptp)
REVERT: D   44 PHE cc_start: 0.8852 (t80) cc_final: 0.8578 (t80)
REVERT: D  105 TYR cc_start: 0.8521 (m-80) cc_final: 0.8154 (m-10)
  outliers start: 8
  outliers final: 8
  residues processed: 75
  average time/residue: 0.0884
  time to fit residues: 7.6880
Evaluate side-chains
  78 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue  115 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 42 optimal weight:    4.9990
   chunk 11 optimal weight:    0.3980
   chunk 5 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 35 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
B  27 ASN
D  98 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.155996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.119878 restraints weight = 4736.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 3.56
r_work: 0.3429 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3478  Z= 0.139
  Angle     :  0.554   6.589   4772  Z= 0.286
  Chirality :  0.049   0.142    554
  Planarity :  0.005   0.049    605
  Dihedral  :  3.862  18.683    498
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.82 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.41), residues: 459
  helix: -1.38 (0.81), residues: 34
  sheet:  0.77 (0.38), residues: 223
  loop : -0.26 (0.43), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  34 
 TYR   0.017   0.001   TYR C 105 
 PHE   0.009   0.001   PHE D  44 
 TRP   0.016   0.001   TRP C  79 
 HIS   0.002   0.001   HIS C  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3478)
  covalent geometry    : angle       0.55427 ( 4772)
  hydrogen bonds       : bond        0.02587 (  120)
  hydrogen bonds       : angle       5.84254 (  396)

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.6436 (ttp) cc_final: 0.5896 (tmm)
REVERT: A   14 VAL cc_start: 0.9027 (t) cc_final: 0.8617 (m)
REVERT: A  103 ARG cc_start: 0.7217 (mpt180) cc_final: 0.6717 (mmt-90)
REVERT: C   15 LYS cc_start: 0.8091 (tmtt) cc_final: 0.7614 (tmtt)
REVERT: C   35 LYS cc_start: 0.7767 (tptm) cc_final: 0.7452 (tptp)
REVERT: C   78 TYR cc_start: 0.7270 (t80) cc_final: 0.6870 (m-80)
REVERT: D   44 PHE cc_start: 0.8853 (t80) cc_final: 0.8538 (t80)
  outliers start: 8
  outliers final: 8
  residues processed: 71
  average time/residue: 0.0995
  time to fit residues: 8.1505
Evaluate side-chains
  74 residues out of total 391 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   52 SER
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue  115 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 38 optimal weight:    0.2980
   chunk 11 optimal weight:    0.0070
   chunk 5 optimal weight:    0.0470
   chunk 8 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
C  27 ASN
D  98 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.161905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.127307 restraints weight = 4766.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 3.59
r_work: 0.3541 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   3478  Z= 0.087
  Angle     :  0.515   6.631   4772  Z= 0.264
  Chirality :  0.047   0.136    554
  Planarity :  0.005   0.052    605
  Dihedral  :  3.624  19.613    498
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.49 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.41), residues: 459
  helix: -1.47 (0.80), residues: 34
  sheet:  0.97 (0.38), residues: 223
  loop : -0.35 (0.42), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  34 
 TYR   0.014   0.001   TYR C 105 
 PHE   0.008   0.001   PHE D  87 
 TRP   0.016   0.001   TRP C  79 
 HIS   0.001   0.000   HIS B  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 ( 3478)
  covalent geometry    : angle       0.51540 ( 4772)
  hydrogen bonds       : bond        0.02179 (  120)
  hydrogen bonds       : angle       5.38468 (  396)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1011.60 seconds
wall clock time: 18 minutes 0.21 seconds (1080.21 seconds total)