Starting phenix.real_space_refine
on Wed Mar  4 00:34:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6v1i_21012/03_2026/6v1i_21012_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6v1i_21012/03_2026/6v1i_21012.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6v1i_21012/03_2026/6v1i_21012.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6v1i_21012/03_2026/6v1i_21012.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6v1i_21012/03_2026/6v1i_21012_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6v1i_21012/03_2026/6v1i_21012_neut.cif"
  }
  resolution = 3.8
  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=   0.001 sd=   0.005
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: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    6129      2.51       5
     N    1701      2.21       5
     O    1827      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 9711
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1079
          Classifications: {'peptide': 137}
          Link IDs: {'PTRANS': 5, 'TRANS': 131}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I
  Time building chain proxies: 1.21, per 1000 atoms: 0.12
  Number of scatterers: 9711
  At special positions: 0
  Unit cell: (133.434, 131.316, 67.776, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1827      8.00
     N    1701      7.00
     C    6129      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: 0.67
  Conformation dependent library (CDL) restraints added in 368.6 milliseconds
  

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2376

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 0 sheets defined
      79.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 15
    Processing helix  chain 'A' and resid 18 through 28
      removed outlier: 3.840A  pdb=" N   LEU A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 51
      removed outlier: 3.715A  pdb=" N   VAL A  42 " --> pdb=" O   GLU A  38 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU A  48 " --> pdb=" O   ALA A  44 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A  49 " --> pdb=" O   GLU A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 94
      removed outlier: 3.859A  pdb=" N   GLU A  62 " --> pdb=" O   ASP A  58 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ALA A  79 " --> pdb=" O   LYS A  75 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ASN A  87 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY A  94 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 137
      removed outlier: 3.612A  pdb=" N   ILE A 112 " --> pdb=" O   ARG A 108 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA A 113 " --> pdb=" O   PRO A 109 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE A 127 " --> pdb=" O   ASP A 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 15
    Processing helix  chain 'B' and resid 18 through 28
      removed outlier: 3.839A  pdb=" N   LEU B  28 " --> pdb=" O   GLN B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 51
      removed outlier: 3.716A  pdb=" N   VAL B  42 " --> pdb=" O   GLU B  38 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU B  48 " --> pdb=" O   ALA B  44 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU B  49 " --> pdb=" O   GLU B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 94
      removed outlier: 3.858A  pdb=" N   GLU B  62 " --> pdb=" O   ASP B  58 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ALA B  79 " --> pdb=" O   LYS B  75 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ASN B  87 " --> pdb=" O   ASN B  83 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY B  94 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 137
      removed outlier: 3.611A  pdb=" N   ILE B 112 " --> pdb=" O   ARG B 108 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA B 113 " --> pdb=" O   PRO B 109 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE B 127 " --> pdb=" O   ASP B 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 5 through 15
    Processing helix  chain 'C' and resid 18 through 28
      removed outlier: 3.840A  pdb=" N   LEU C  28 " --> pdb=" O   GLN C  24 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 51
      removed outlier: 3.716A  pdb=" N   VAL C  42 " --> pdb=" O   GLU C  38 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU C  48 " --> pdb=" O   ALA C  44 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU C  49 " --> pdb=" O   GLU C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 94
      removed outlier: 3.859A  pdb=" N   GLU C  62 " --> pdb=" O   ASP C  58 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ALA C  79 " --> pdb=" O   LYS C  75 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ASN C  87 " --> pdb=" O   ASN C  83 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY C  94 " --> pdb=" O   ALA C  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 108 through 137
      removed outlier: 3.612A  pdb=" N   ILE C 112 " --> pdb=" O   ARG C 108 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA C 113 " --> pdb=" O   PRO C 109 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE C 127 " --> pdb=" O   ASP C 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 5 through 15
    Processing helix  chain 'D' and resid 18 through 28
      removed outlier: 3.839A  pdb=" N   LEU D  28 " --> pdb=" O   GLN D  24 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 35 through 51
      removed outlier: 3.716A  pdb=" N   VAL D  42 " --> pdb=" O   GLU D  38 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU D  48 " --> pdb=" O   ALA D  44 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU D  49 " --> pdb=" O   GLU D  45 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 94
      removed outlier: 3.859A  pdb=" N   GLU D  62 " --> pdb=" O   ASP D  58 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA D  79 " --> pdb=" O   LYS D  75 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ASN D  87 " --> pdb=" O   ASN D  83 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY D  94 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 108 through 137
      removed outlier: 3.611A  pdb=" N   ILE D 112 " --> pdb=" O   ARG D 108 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA D 113 " --> pdb=" O   PRO D 109 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE D 127 " --> pdb=" O   ASP D 123 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 5 through 15
    Processing helix  chain 'E' and resid 18 through 28
      removed outlier: 3.840A  pdb=" N   LEU E  28 " --> pdb=" O   GLN E  24 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 35 through 51
      removed outlier: 3.716A  pdb=" N   VAL E  42 " --> pdb=" O   GLU E  38 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU E  48 " --> pdb=" O   ALA E  44 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU E  49 " --> pdb=" O   GLU E  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 94
      removed outlier: 3.859A  pdb=" N   GLU E  62 " --> pdb=" O   ASP E  58 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA E  79 " --> pdb=" O   LYS E  75 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ASN E  87 " --> pdb=" O   ASN E  83 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY E  94 " --> pdb=" O   ALA E  90 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 108 through 137
      removed outlier: 3.611A  pdb=" N   ILE E 112 " --> pdb=" O   ARG E 108 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA E 113 " --> pdb=" O   PRO E 109 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE E 127 " --> pdb=" O   ASP E 123 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 5 through 15
    Processing helix  chain 'F' and resid 18 through 28
      removed outlier: 3.840A  pdb=" N   LEU F  28 " --> pdb=" O   GLN F  24 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 35 through 51
      removed outlier: 3.715A  pdb=" N   VAL F  42 " --> pdb=" O   GLU F  38 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU F  48 " --> pdb=" O   ALA F  44 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU F  49 " --> pdb=" O   GLU F  45 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 55 through 94
      removed outlier: 3.859A  pdb=" N   GLU F  62 " --> pdb=" O   ASP F  58 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA F  79 " --> pdb=" O   LYS F  75 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ASN F  87 " --> pdb=" O   ASN F  83 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY F  94 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 108 through 137
      removed outlier: 3.611A  pdb=" N   ILE F 112 " --> pdb=" O   ARG F 108 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA F 113 " --> pdb=" O   PRO F 109 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE F 127 " --> pdb=" O   ASP F 123 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 5 through 15
    Processing helix  chain 'G' and resid 18 through 28
      removed outlier: 3.840A  pdb=" N   LEU G  28 " --> pdb=" O   GLN G  24 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 35 through 51
      removed outlier: 3.715A  pdb=" N   VAL G  42 " --> pdb=" O   GLU G  38 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU G  48 " --> pdb=" O   ALA G  44 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU G  49 " --> pdb=" O   GLU G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 94
      removed outlier: 3.859A  pdb=" N   GLU G  62 " --> pdb=" O   ASP G  58 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ALA G  79 " --> pdb=" O   LYS G  75 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ASN G  87 " --> pdb=" O   ASN G  83 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLY G  94 " --> pdb=" O   ALA G  90 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 108 through 137
      removed outlier: 3.612A  pdb=" N   ILE G 112 " --> pdb=" O   ARG G 108 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA G 113 " --> pdb=" O   PRO G 109 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE G 127 " --> pdb=" O   ASP G 123 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 5 through 15
    Processing helix  chain 'H' and resid 18 through 28
      removed outlier: 3.840A  pdb=" N   LEU H  28 " --> pdb=" O   GLN H  24 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 35 through 51
      removed outlier: 3.716A  pdb=" N   VAL H  42 " --> pdb=" O   GLU H  38 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLU H  48 " --> pdb=" O   ALA H  44 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU H  49 " --> pdb=" O   GLU H  45 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 94
      removed outlier: 3.858A  pdb=" N   GLU H  62 " --> pdb=" O   ASP H  58 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA H  79 " --> pdb=" O   LYS H  75 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ASN H  87 " --> pdb=" O   ASN H  83 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY H  94 " --> pdb=" O   ALA H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 108 through 137
      removed outlier: 3.611A  pdb=" N   ILE H 112 " --> pdb=" O   ARG H 108 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA H 113 " --> pdb=" O   PRO H 109 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE H 127 " --> pdb=" O   ASP H 123 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 5 through 15
    Processing helix  chain 'I' and resid 18 through 28
      removed outlier: 3.840A  pdb=" N   LEU I  28 " --> pdb=" O   GLN I  24 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 35 through 51
      removed outlier: 3.716A  pdb=" N   VAL I  42 " --> pdb=" O   GLU I  38 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU I  48 " --> pdb=" O   ALA I  44 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU I  49 " --> pdb=" O   GLU I  45 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 55 through 94
      removed outlier: 3.859A  pdb=" N   GLU I  62 " --> pdb=" O   ASP I  58 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ALA I  79 " --> pdb=" O   LYS I  75 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ASN I  87 " --> pdb=" O   ASN I  83 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY I  94 " --> pdb=" O   ALA I  90 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 108 through 137
      removed outlier: 3.612A  pdb=" N   ILE I 112 " --> pdb=" O   ARG I 108 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA I 113 " --> pdb=" O   PRO I 109 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE I 127 " --> pdb=" O   ASP I 123 " (cutoff:3.500A)

    702 hydrogen bonds defined for protein.
    2106 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: 1.29

  Time building geometry restraints manager: 0.93 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: 3313
        1.34 -     1.46: 1038
        1.46 -     1.57: 5360
        1.57 -     1.68: 0
        1.68 -     1.80: 108
  Bond restraints: 9819
  Sorted by residual:
  bond pdb=" C   SER I   4 "
       pdb=" N   PHE I   5 "
    ideal  model  delta    sigma   weight residual
    1.332  1.302  0.030 1.35e-02 5.49e+03 4.82e+00
  bond pdb=" C   SER E   4 "
       pdb=" N   PHE E   5 "
    ideal  model  delta    sigma   weight residual
    1.331  1.301  0.029 1.38e-02 5.25e+03 4.46e+00
  bond pdb=" C   SER D   4 "
       pdb=" N   PHE D   5 "
    ideal  model  delta    sigma   weight residual
    1.331  1.302  0.029 1.38e-02 5.25e+03 4.41e+00
  bond pdb=" C   SER G   4 "
       pdb=" N   PHE G   5 "
    ideal  model  delta    sigma   weight residual
    1.331  1.302  0.029 1.38e-02 5.25e+03 4.34e+00
  bond pdb=" C   SER C   4 "
       pdb=" N   PHE C   5 "
    ideal  model  delta    sigma   weight residual
    1.331  1.302  0.029 1.38e-02 5.25e+03 4.32e+00
  ... (remaining 9814 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.16: 11472
        1.16 -     2.33: 1305
        2.33 -     3.49: 336
        3.49 -     4.65: 117
        4.65 -     5.82: 18
  Bond angle restraints: 13248
  Sorted by residual:
  angle pdb=" C   GLU B  97 "
        pdb=" N   HIS B  98 "
        pdb=" CA  HIS B  98 "
      ideal   model   delta    sigma   weight residual
     121.03  124.60   -3.57 1.60e+00 3.91e-01 4.99e+00
  angle pdb=" C   GLU F  97 "
        pdb=" N   HIS F  98 "
        pdb=" CA  HIS F  98 "
      ideal   model   delta    sigma   weight residual
     121.03  124.59   -3.56 1.60e+00 3.91e-01 4.96e+00
  angle pdb=" C   GLU I  97 "
        pdb=" N   HIS I  98 "
        pdb=" CA  HIS I  98 "
      ideal   model   delta    sigma   weight residual
     121.03  124.59   -3.56 1.60e+00 3.91e-01 4.96e+00
  angle pdb=" C   GLU A  97 "
        pdb=" N   HIS A  98 "
        pdb=" CA  HIS A  98 "
      ideal   model   delta    sigma   weight residual
     121.03  124.58   -3.55 1.60e+00 3.91e-01 4.93e+00
  angle pdb=" C   GLU G  97 "
        pdb=" N   HIS G  98 "
        pdb=" CA  HIS G  98 "
      ideal   model   delta    sigma   weight residual
     121.03  124.57   -3.54 1.60e+00 3.91e-01 4.89e+00
  ... (remaining 13243 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.54: 5850
       13.54 -    27.08: 216
       27.08 -    40.62: 126
       40.62 -    54.16: 0
       54.16 -    67.70: 9
  Dihedral angle restraints: 6201
    sinusoidal: 2574
      harmonic: 3627
  Sorted by residual:
  dihedral pdb=" CA  LEU F  15 "
           pdb=" C   LEU F  15 "
           pdb=" N   GLY F  16 "
           pdb=" CA  GLY F  16 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.10   15.90     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CA  LEU H  15 "
           pdb=" C   LEU H  15 "
           pdb=" N   GLY H  16 "
           pdb=" CA  GLY H  16 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.11   15.89     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CA  LEU C  15 "
           pdb=" C   LEU C  15 "
           pdb=" N   GLY C  16 "
           pdb=" CA  GLY C  16 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.12   15.88     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 6198 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 753
       0.026 -    0.051: 446
       0.051 -    0.076: 250
       0.076 -    0.102: 83
       0.102 -    0.127: 52
  Chirality restraints: 1584
  Sorted by residual:
  chirality pdb=" CA  ILE I 105 "
            pdb=" N   ILE I 105 "
            pdb=" C   ILE I 105 "
            pdb=" CB  ILE I 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  ILE C 105 "
            pdb=" N   ILE C 105 "
            pdb=" C   ILE C 105 "
            pdb=" CB  ILE C 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.03e-01
  chirality pdb=" CA  ILE A 105 "
            pdb=" N   ILE A 105 "
            pdb=" C   ILE A 105 "
            pdb=" CB  ILE A 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.00e-01
  ... (remaining 1581 not shown)

  Planarity restraints: 1710
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS C  98 "   -0.028 5.00e-02 4.00e+02   4.19e-02 2.81e+00
        pdb=" N   PRO C  99 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO C  99 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C  99 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS D  98 "   -0.028 5.00e-02 4.00e+02   4.19e-02 2.81e+00
        pdb=" N   PRO D  99 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO D  99 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO D  99 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS E  98 "   -0.028 5.00e-02 4.00e+02   4.19e-02 2.81e+00
        pdb=" N   PRO E  99 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO E  99 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO E  99 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1707 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 3982
        2.98 -     3.46: 10365
        3.46 -     3.94: 14573
        3.94 -     4.42: 17338
        4.42 -     4.90: 26850
  Nonbonded interactions: 73108
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN E  87 "
            pdb=" NE2 HIS E  98 "
     model   vdw
     2.505 3.120
  nonbonded pdb=" OD1 ASN G  87 "
            pdb=" NE2 HIS G  98 "
     model   vdw
     2.505 3.120
  nonbonded pdb=" OD1 ASN F  87 "
            pdb=" NE2 HIS F  98 "
     model   vdw
     2.505 3.120
  nonbonded pdb=" OD1 ASN A  87 "
            pdb=" NE2 HIS A  98 "
     model   vdw
     2.505 3.120
  nonbonded pdb=" OD1 ASN I  87 "
            pdb=" NE2 HIS I  98 "
     model   vdw
     2.505 3.120
  ... (remaining 73103 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
}

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 group one per residue
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:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.750
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8859
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      :  0.007   0.042   9819  Z= 0.320
  Angle     :  0.905   5.817  13248  Z= 0.507
  Chirality :  0.044   0.127   1584
  Planarity :  0.006   0.042   1710
  Dihedral  :  9.434  67.700   3825
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 1.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  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 are not related in a simple way.
  whole: -3.88 (0.19), residues: 1215
  helix: -2.88 (0.11), residues: 972
  sheet:  None (None), residues: 0
  loop :  0.17 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F  69 
 TYR   0.006   0.002   TYR E  13 
 PHE   0.008   0.002   PHE C  73 
 HIS   0.006   0.002   HIS G  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00705 ( 9819)
  covalent geometry    : angle       0.90488 (13248)
  hydrogen bonds       : bond        0.30005 (  702)
  hydrogen bonds       : angle       8.67693 ( 2106)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 322
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 ASP cc_start: 0.8579 (m-30) cc_final: 0.8299 (m-30)
REVERT: A  117 ASP cc_start: 0.8466 (t0) cc_final: 0.8215 (t0)
REVERT: B   72 ILE cc_start: 0.9547 (mm) cc_final: 0.9299 (mm)
REVERT: C   72 ILE cc_start: 0.9479 (mm) cc_final: 0.9255 (mm)
REVERT: D   72 ILE cc_start: 0.9506 (mm) cc_final: 0.9236 (mm)
REVERT: E   76 ASP cc_start: 0.8587 (m-30) cc_final: 0.8347 (m-30)
REVERT: F   72 ILE cc_start: 0.9539 (mm) cc_final: 0.9301 (mt)
REVERT: F  123 ASP cc_start: 0.8895 (t0) cc_final: 0.8583 (t0)
REVERT: G   72 ILE cc_start: 0.9494 (mm) cc_final: 0.9262 (mt)
REVERT: G  117 ASP cc_start: 0.8604 (t0) cc_final: 0.8201 (t0)
REVERT: H   72 ILE cc_start: 0.9501 (mm) cc_final: 0.9295 (mm)
REVERT: H   76 ASP cc_start: 0.8573 (m-30) cc_final: 0.8276 (m-30)
REVERT: I    1 MET cc_start: 0.6519 (ttm) cc_final: 0.4992 (mtp)
REVERT: I   24 GLN cc_start: 0.9317 (mt0) cc_final: 0.9083 (mt0)
REVERT: I   72 ILE cc_start: 0.9536 (mm) cc_final: 0.9292 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 322
  average time/residue: 0.1640
  time to fit residues: 64.5783
Evaluate side-chains
  182 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0060
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.042087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.031486 restraints weight = 56963.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.032557 restraints weight = 33558.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.033262 restraints weight = 24496.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.033686 restraints weight = 20136.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.034006 restraints weight = 17901.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8768
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9819  Z= 0.129
  Angle     :  0.538   4.321  13248  Z= 0.292
  Chirality :  0.039   0.117   1584
  Planarity :  0.005   0.031   1710
  Dihedral  :  3.831  10.279   1350
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  :  9.69 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.22), residues: 1215
  helix:  0.65 (0.15), residues: 972
  sheet:  None (None), residues: 0
  loop :  0.90 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G 108 
 TYR   0.005   0.001   TYR C  88 
 PHE   0.005   0.001   PHE E  73 
 HIS   0.001   0.000   HIS H  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9819)
  covalent geometry    : angle       0.53789 (13248)
  hydrogen bonds       : bond        0.04898 (  702)
  hydrogen bonds       : angle       4.06757 ( 2106)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 206
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 ASP cc_start: 0.8489 (m-30) cc_final: 0.8246 (m-30)
REVERT: A  117 ASP cc_start: 0.8497 (t0) cc_final: 0.8260 (t0)
REVERT: A  120 MET cc_start: 0.8763 (mtp) cc_final: 0.8343 (mtp)
REVERT: B    1 MET cc_start: 0.5899 (ttt) cc_final: 0.5021 (ttt)
REVERT: D    6 ARG cc_start: 0.7778 (mmt180) cc_final: 0.7281 (mmt180)
REVERT: D  120 MET cc_start: 0.8607 (mtp) cc_final: 0.8333 (mtm)
REVERT: E    4 SER cc_start: 0.8631 (m) cc_final: 0.8394 (p)
REVERT: E   75 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8961 (mmtt)
REVERT: E   76 ASP cc_start: 0.8475 (m-30) cc_final: 0.8247 (m-30)
REVERT: E   92 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7962 (tmm)
REVERT: F   72 ILE cc_start: 0.9458 (mm) cc_final: 0.9242 (tp)
REVERT: F  117 ASP cc_start: 0.8408 (t0) cc_final: 0.8166 (t0)
REVERT: F  120 MET cc_start: 0.8697 (mtp) cc_final: 0.7979 (mtp)
REVERT: G   33 LYS cc_start: 0.8301 (ptmm) cc_final: 0.7983 (ttpp)
REVERT: G  115 MET cc_start: 0.9179 (mmt) cc_final: 0.8972 (mmt)
REVERT: G  117 ASP cc_start: 0.8565 (t0) cc_final: 0.8225 (t0)
REVERT: H    4 SER cc_start: 0.8633 (m) cc_final: 0.8429 (p)
REVERT: H   76 ASP cc_start: 0.8439 (m-30) cc_final: 0.8132 (m-30)
REVERT: I  117 ASP cc_start: 0.8416 (t0) cc_final: 0.8206 (t0)
  outliers start: 41
  outliers final: 30
  residues processed: 235
  average time/residue: 0.1584
  time to fit residues: 46.3881
Evaluate side-chains
  179 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 148
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain E residue    3 VAL
Chi-restraints excluded: chain E residue   35 THR
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain E residue   92 MET
Chi-restraints excluded: chain E residue  105 ILE
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   55 SER
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   35 THR
Chi-restraints excluded: chain G residue   55 SER
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue  105 ILE
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   35 THR
Chi-restraints excluded: chain I residue   55 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0970
   chunk 27 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 68 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9980
   chunk 110 optimal weight:    1.9990
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  83 ASN
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  83 ASN
C  82 GLN
C  83 ASN
D  82 GLN
D  83 ASN
E  83 ASN
** F  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  83 ASN
** G  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  83 ASN
H  82 GLN
H  83 ASN
** I  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  83 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.041083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2577 r_free = 0.2577 target = 0.030319 restraints weight = 57356.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.031364 restraints weight = 33681.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.032045 restraints weight = 24553.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.032431 restraints weight = 20293.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.032732 restraints weight = 18151.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8827
moved from start:          0.4344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9819  Z= 0.107
  Angle     :  0.477   6.616  13248  Z= 0.252
  Chirality :  0.037   0.128   1584
  Planarity :  0.004   0.028   1710
  Dihedral  :  3.322   9.883   1350
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 11.97 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.10 (0.23), residues: 1215
  helix:  2.24 (0.16), residues: 963
  sheet:  None (None), residues: 0
  loop :  1.50 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G 108 
 TYR   0.005   0.001   TYR G  81 
 PHE   0.006   0.001   PHE H  73 
 HIS   0.003   0.000   HIS B  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 9819)
  covalent geometry    : angle       0.47676 (13248)
  hydrogen bonds       : bond        0.03688 (  702)
  hydrogen bonds       : angle       3.71366 ( 2106)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 164
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 SER cc_start: 0.8474 (m) cc_final: 0.8196 (p)
REVERT: A   75 LYS cc_start: 0.9371 (mmmt) cc_final: 0.9141 (tppt)
REVERT: B  117 ASP cc_start: 0.8370 (t0) cc_final: 0.8157 (t0)
REVERT: B  120 MET cc_start: 0.8984 (mtp) cc_final: 0.8605 (mtp)
REVERT: D    4 SER cc_start: 0.8613 (m) cc_final: 0.8389 (p)
REVERT: D    6 ARG cc_start: 0.7826 (mmt180) cc_final: 0.7298 (mmt180)
REVERT: E   92 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8033 (tmm)
REVERT: G   33 LYS cc_start: 0.8242 (ptmm) cc_final: 0.7856 (ttpp)
REVERT: G  117 ASP cc_start: 0.8517 (t0) cc_final: 0.8253 (t0)
REVERT: H   76 ASP cc_start: 0.8515 (m-30) cc_final: 0.8181 (m-30)
REVERT: I  120 MET cc_start: 0.9028 (mtp) cc_final: 0.8735 (mtm)
  outliers start: 35
  outliers final: 33
  residues processed: 188
  average time/residue: 0.1425
  time to fit residues: 33.7054
Evaluate side-chains
  171 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 137
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain E residue    3 VAL
Chi-restraints excluded: chain E residue    7 ASP
Chi-restraints excluded: chain E residue   35 THR
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain E residue   92 MET
Chi-restraints excluded: chain E residue  105 ILE
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   55 SER
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue    7 ASP
Chi-restraints excluded: chain G residue   35 THR
Chi-restraints excluded: chain G residue   55 SER
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue    7 ASP
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue  105 ILE
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   35 THR
Chi-restraints excluded: chain I residue   55 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 116 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  82 GLN
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  82 GLN
G  82 GLN
I  82 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.041101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2573 r_free = 0.2573 target = 0.030146 restraints weight = 57661.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.031186 restraints weight = 34037.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.031869 restraints weight = 24884.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.032271 restraints weight = 20621.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.032492 restraints weight = 18452.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8841
moved from start:          0.4609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9819  Z= 0.105
  Angle     :  0.478   8.064  13248  Z= 0.244
  Chirality :  0.036   0.129   1584
  Planarity :  0.004   0.028   1710
  Dihedral  :  3.112   8.998   1350
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 11.97 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.11 (0.24), residues: 1215
  helix:  3.01 (0.16), residues: 963
  sheet:  None (None), residues: 0
  loop :  1.63 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F   8 
 TYR   0.005   0.001   TYR I  81 
 PHE   0.007   0.001   PHE H  73 
 HIS   0.001   0.000   HIS G  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 9819)
  covalent geometry    : angle       0.47846 (13248)
  hydrogen bonds       : bond        0.03280 (  702)
  hydrogen bonds       : angle       3.58896 ( 2106)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 156
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 SER cc_start: 0.8456 (m) cc_final: 0.8256 (p)
REVERT: A   75 LYS cc_start: 0.9409 (mmmt) cc_final: 0.9145 (tppt)
REVERT: C  120 MET cc_start: 0.8897 (mtp) cc_final: 0.8537 (mtp)
REVERT: G  117 ASP cc_start: 0.8506 (t0) cc_final: 0.8230 (t0)
REVERT: H    8 ARG cc_start: 0.9321 (mmm-85) cc_final: 0.8996 (mmm-85)
REVERT: H   76 ASP cc_start: 0.8504 (m-30) cc_final: 0.8276 (m-30)
  outliers start: 33
  outliers final: 30
  residues processed: 179
  average time/residue: 0.1536
  time to fit residues: 34.5135
Evaluate side-chains
  172 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 142
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain E residue    3 VAL
Chi-restraints excluded: chain E residue    7 ASP
Chi-restraints excluded: chain E residue   35 THR
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain E residue  105 ILE
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   55 SER
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   35 THR
Chi-restraints excluded: chain G residue   55 SER
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue  105 ILE
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   35 THR
Chi-restraints excluded: chain I residue   55 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 113 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 49 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 95 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 124 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.040713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2555 r_free = 0.2555 target = 0.029815 restraints weight = 58241.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.030849 restraints weight = 34714.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.031510 restraints weight = 25545.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.031851 restraints weight = 21219.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.032161 restraints weight = 19155.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.2643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8845
moved from start:          0.4786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9819  Z= 0.106
  Angle     :  0.499   9.938  13248  Z= 0.247
  Chirality :  0.036   0.133   1584
  Planarity :  0.004   0.028   1710
  Dihedral  :  3.020   8.772   1350
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 10.92 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.49 (0.24), residues: 1215
  helix:  3.28 (0.16), residues: 963
  sheet:  None (None), residues: 0
  loop :  1.72 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 108 
 TYR   0.005   0.001   TYR I  81 
 PHE   0.006   0.001   PHE F  73 
 HIS   0.002   0.000   HIS C  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 9819)
  covalent geometry    : angle       0.49869 (13248)
  hydrogen bonds       : bond        0.03182 (  702)
  hydrogen bonds       : angle       3.51957 ( 2106)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 143
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 LYS cc_start: 0.9415 (mmmt) cc_final: 0.9161 (tppt)
REVERT: B  120 MET cc_start: 0.8781 (mtp) cc_final: 0.8520 (mtp)
REVERT: C  120 MET cc_start: 0.8838 (mtp) cc_final: 0.8436 (mtp)
REVERT: G    8 ARG cc_start: 0.9348 (mmm-85) cc_final: 0.9050 (mmm-85)
REVERT: G  117 ASP cc_start: 0.8563 (t0) cc_final: 0.8286 (t0)
REVERT: H    8 ARG cc_start: 0.9337 (mmm-85) cc_final: 0.9023 (mmm-85)
REVERT: H   75 LYS cc_start: 0.9442 (mmmt) cc_final: 0.9138 (tppt)
REVERT: H   76 ASP cc_start: 0.8573 (m-30) cc_final: 0.8276 (m-30)
REVERT: I    8 ARG cc_start: 0.9220 (mmm-85) cc_final: 0.8933 (mmm-85)
  outliers start: 45
  outliers final: 31
  residues processed: 175
  average time/residue: 0.1333
  time to fit residues: 29.8186
Evaluate side-chains
  169 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 138
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain B residue    3 VAL
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain E residue    3 VAL
Chi-restraints excluded: chain E residue    7 ASP
Chi-restraints excluded: chain E residue   35 THR
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain E residue  105 ILE
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   55 SER
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue    7 ASP
Chi-restraints excluded: chain G residue   35 THR
Chi-restraints excluded: chain G residue   55 SER
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue  105 ILE
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   35 THR
Chi-restraints excluded: chain I residue   55 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 115 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 39 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9980
   chunk 83 optimal weight:    0.0000
   chunk 17 optimal weight:    3.9990
   chunk 94 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9980
   chunk 113 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.040536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2566 r_free = 0.2566 target = 0.029814 restraints weight = 58051.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2608 r_free = 0.2608 target = 0.030838 restraints weight = 33750.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.031498 restraints weight = 24600.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.031883 restraints weight = 20383.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2661 r_free = 0.2661 target = 0.032163 restraints weight = 18266.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8836
moved from start:          0.5021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9819  Z= 0.100
  Angle     :  0.496  10.175  13248  Z= 0.244
  Chirality :  0.036   0.129   1584
  Planarity :  0.004   0.028   1710
  Dihedral  :  2.961   8.732   1350
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 11.59 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.68 (0.24), residues: 1215
  helix:  3.42 (0.16), residues: 963
  sheet:  None (None), residues: 0
  loop :  1.75 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 108 
 TYR   0.004   0.001   TYR I  81 
 PHE   0.007   0.001   PHE B  73 
 HIS   0.001   0.000   HIS B  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 9819)
  covalent geometry    : angle       0.49566 (13248)
  hydrogen bonds       : bond        0.03062 (  702)
  hydrogen bonds       : angle       3.42565 ( 2106)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 147
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 LYS cc_start: 0.9411 (mmmt) cc_final: 0.8991 (tppt)
REVERT: A  135 LYS cc_start: 0.9387 (tptp) cc_final: 0.9070 (ptpp)
REVERT: B    8 ARG cc_start: 0.9386 (mmm-85) cc_final: 0.9077 (mmm-85)
REVERT: B  120 MET cc_start: 0.8752 (mtp) cc_final: 0.8524 (mtp)
REVERT: B  135 LYS cc_start: 0.9513 (tptp) cc_final: 0.8990 (ptpp)
REVERT: C  135 LYS cc_start: 0.9427 (tptp) cc_final: 0.9028 (ptpp)
REVERT: D  120 MET cc_start: 0.9103 (mpp) cc_final: 0.8826 (mpp)
REVERT: E   75 LYS cc_start: 0.9392 (mmmt) cc_final: 0.9144 (tptt)
REVERT: F   24 GLN cc_start: 0.8761 (mt0) cc_final: 0.8512 (mt0)
REVERT: F   75 LYS cc_start: 0.9431 (mmmt) cc_final: 0.9016 (tppt)
REVERT: G    8 ARG cc_start: 0.9324 (mmm-85) cc_final: 0.9037 (mmm-85)
REVERT: G  117 ASP cc_start: 0.8449 (t0) cc_final: 0.8216 (t0)
REVERT: G  135 LYS cc_start: 0.9378 (tptp) cc_final: 0.9070 (ptpp)
REVERT: H    8 ARG cc_start: 0.9300 (mmm-85) cc_final: 0.8991 (mmm-85)
REVERT: H   24 GLN cc_start: 0.8889 (mt0) cc_final: 0.8561 (mt0)
REVERT: H   75 LYS cc_start: 0.9427 (mmmt) cc_final: 0.9135 (tppt)
REVERT: H   76 ASP cc_start: 0.8512 (m-30) cc_final: 0.8270 (m-30)
REVERT: H  135 LYS cc_start: 0.9452 (tptp) cc_final: 0.9034 (ptpp)
REVERT: I    8 ARG cc_start: 0.9219 (mmm-85) cc_final: 0.8994 (mmm-85)
  outliers start: 36
  outliers final: 30
  residues processed: 171
  average time/residue: 0.1322
  time to fit residues: 29.1409
Evaluate side-chains
  171 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 141
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain E residue    7 ASP
Chi-restraints excluded: chain E residue   35 THR
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain E residue  105 ILE
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   55 SER
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue    7 ASP
Chi-restraints excluded: chain G residue   35 THR
Chi-restraints excluded: chain G residue   55 SER
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue  105 ILE
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   35 THR
Chi-restraints excluded: chain I residue   55 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 109 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 61 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   chunk 100 optimal weight:    0.0770
   chunk 84 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.9942

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.040268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2548 r_free = 0.2548 target = 0.029391 restraints weight = 57848.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2589 r_free = 0.2589 target = 0.030386 restraints weight = 34241.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.031045 restraints weight = 25144.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.031379 restraints weight = 20908.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.031663 restraints weight = 18937.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8852
moved from start:          0.5102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9819  Z= 0.108
  Angle     :  0.515  10.801  13248  Z= 0.250
  Chirality :  0.036   0.127   1584
  Planarity :  0.004   0.027   1710
  Dihedral  :  2.938   8.976   1350
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 12.16 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.79 (0.24), residues: 1215
  helix:  3.51 (0.16), residues: 963
  sheet:  None (None), residues: 0
  loop :  1.74 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 108 
 TYR   0.005   0.001   TYR I  81 
 PHE   0.007   0.001   PHE B  73 
 HIS   0.001   0.000   HIS B  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 9819)
  covalent geometry    : angle       0.51510 (13248)
  hydrogen bonds       : bond        0.03083 (  702)
  hydrogen bonds       : angle       3.45015 ( 2106)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 146
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 LYS cc_start: 0.9440 (mmmt) cc_final: 0.9184 (tppt)
REVERT: A  135 LYS cc_start: 0.9428 (tptp) cc_final: 0.9128 (ptpp)
REVERT: B    8 ARG cc_start: 0.9400 (mmm-85) cc_final: 0.9082 (mmm-85)
REVERT: B  120 MET cc_start: 0.8718 (mtp) cc_final: 0.8483 (mtp)
REVERT: B  135 LYS cc_start: 0.9500 (tptp) cc_final: 0.8987 (ptpp)
REVERT: C  135 LYS cc_start: 0.9452 (tptp) cc_final: 0.9044 (ptpp)
REVERT: E   75 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9147 (tptt)
REVERT: F   24 GLN cc_start: 0.8752 (mt0) cc_final: 0.8489 (mt0)
REVERT: G  117 ASP cc_start: 0.8447 (t0) cc_final: 0.8119 (t0)
REVERT: H   24 GLN cc_start: 0.8902 (mt0) cc_final: 0.8563 (mt0)
REVERT: H   75 LYS cc_start: 0.9405 (mmmt) cc_final: 0.9172 (tptt)
REVERT: H   76 ASP cc_start: 0.8520 (m-30) cc_final: 0.8256 (m-30)
REVERT: H  135 LYS cc_start: 0.9462 (tptp) cc_final: 0.9028 (ptpp)
REVERT: I    8 ARG cc_start: 0.9255 (mmm-85) cc_final: 0.8987 (mmm-85)
  outliers start: 37
  outliers final: 29
  residues processed: 169
  average time/residue: 0.1402
  time to fit residues: 30.3521
Evaluate side-chains
  172 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 142
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   33 LYS
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain E residue    7 ASP
Chi-restraints excluded: chain E residue   35 THR
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain E residue   75 LYS
Chi-restraints excluded: chain E residue  105 ILE
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   55 SER
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue    7 ASP
Chi-restraints excluded: chain G residue   35 THR
Chi-restraints excluded: chain G residue   55 SER
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue  105 ILE
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   35 THR
Chi-restraints excluded: chain I residue   55 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 16 optimal weight:    9.9990
   chunk 9 optimal weight:    0.0770
   chunk 90 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 116 optimal weight:    6.9990
   chunk 71 optimal weight:    0.6980
   chunk 88 optimal weight:    0.0470
   chunk 8 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   overall best weight:    0.5036

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

Flipped N/Q/H residues before XYZ refinement:
B  82 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.040601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2571 r_free = 0.2571 target = 0.029875 restraints weight = 58106.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.030892 restraints weight = 34244.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.031561 restraints weight = 25035.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.031900 restraints weight = 20686.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.032015 restraints weight = 18664.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8838
moved from start:          0.5291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9819  Z= 0.097
  Angle     :  0.514  11.719  13248  Z= 0.249
  Chirality :  0.036   0.125   1584
  Planarity :  0.004   0.027   1710
  Dihedral  :  2.907  10.675   1350
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 12.54 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.93 (0.24), residues: 1215
  helix:  3.60 (0.16), residues: 963
  sheet:  None (None), residues: 0
  loop :  1.83 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F   8 
 TYR   0.004   0.000   TYR E  81 
 PHE   0.006   0.001   PHE D  73 
 HIS   0.001   0.000   HIS B  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 9819)
  covalent geometry    : angle       0.51409 (13248)
  hydrogen bonds       : bond        0.02871 (  702)
  hydrogen bonds       : angle       3.45134 ( 2106)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 154
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 LYS cc_start: 0.9440 (mmmt) cc_final: 0.9015 (tppt)
REVERT: A  117 ASP cc_start: 0.8324 (t0) cc_final: 0.8051 (m-30)
REVERT: B    8 ARG cc_start: 0.9374 (mmm-85) cc_final: 0.9097 (mmm-85)
REVERT: B  120 MET cc_start: 0.8569 (mtp) cc_final: 0.8327 (mtp)
REVERT: B  135 LYS cc_start: 0.9483 (tptp) cc_final: 0.8996 (ptpp)
REVERT: E   75 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9125 (tptt)
REVERT: F   24 GLN cc_start: 0.8744 (mt0) cc_final: 0.8489 (mt0)
REVERT: F   75 LYS cc_start: 0.9404 (mmmt) cc_final: 0.8984 (tppt)
REVERT: H    8 ARG cc_start: 0.9311 (mmm-85) cc_final: 0.9035 (mmm-85)
REVERT: H   75 LYS cc_start: 0.9399 (mmmt) cc_final: 0.9187 (tptt)
REVERT: H  135 LYS cc_start: 0.9471 (tptp) cc_final: 0.9079 (ptpp)
REVERT: I    8 ARG cc_start: 0.9251 (mmm-85) cc_final: 0.8974 (mmm-85)
  outliers start: 31
  outliers final: 28
  residues processed: 177
  average time/residue: 0.1447
  time to fit residues: 32.4173
Evaluate side-chains
  166 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 137
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   55 SER
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   55 SER
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain E residue   35 THR
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain E residue   75 LYS
Chi-restraints excluded: chain E residue  105 ILE
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue   55 SER
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain F residue  117 ASP
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue    7 ASP
Chi-restraints excluded: chain G residue   35 THR
Chi-restraints excluded: chain G residue   55 SER
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue  105 ILE
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   35 THR
Chi-restraints excluded: chain I residue   55 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 113 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0030
   chunk 43 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0770
   chunk 3 optimal weight:    8.9990
   chunk 99 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9980
   chunk 109 optimal weight:    0.1980
   overall best weight:    0.3948

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.040624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2575 r_free = 0.2575 target = 0.029986 restraints weight = 58100.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.030974 restraints weight = 34361.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.031631 restraints weight = 25164.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.031970 restraints weight = 20862.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.032295 restraints weight = 18810.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8826
moved from start:          0.5455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9819  Z= 0.103
  Angle     :  0.560  12.145  13248  Z= 0.271
  Chirality :  0.036   0.124   1584
  Planarity :  0.004   0.033   1710
  Dihedral  :  2.899   9.630   1350
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 14.43 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.96 (0.23), residues: 1215
  helix:  3.62 (0.16), residues: 963
  sheet:  None (None), residues: 0
  loop :  1.87 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G 108 
 TYR   0.004   0.000   TYR B  81 
 PHE   0.006   0.001   PHE E  73 
 HIS   0.001   0.000   HIS B  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 9819)
  covalent geometry    : angle       0.55968 (13248)
  hydrogen bonds       : bond        0.02873 (  702)
  hydrogen bonds       : angle       3.54439 ( 2106)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 LYS cc_start: 0.9442 (mmmt) cc_final: 0.9119 (tppt)
REVERT: A  117 ASP cc_start: 0.8326 (t0) cc_final: 0.8058 (m-30)
REVERT: A  135 LYS cc_start: 0.9478 (tptp) cc_final: 0.9074 (ptpp)
REVERT: B    8 ARG cc_start: 0.9350 (mmm-85) cc_final: 0.9072 (mmm-85)
REVERT: B  120 MET cc_start: 0.8481 (mtp) cc_final: 0.8270 (mtp)
REVERT: B  135 LYS cc_start: 0.9478 (tptp) cc_final: 0.9011 (ptpp)
REVERT: E    8 ARG cc_start: 0.9281 (mmm-85) cc_final: 0.8905 (mmm-85)
REVERT: E   75 LYS cc_start: 0.9391 (mmmt) cc_final: 0.9147 (tptt)
REVERT: E  117 ASP cc_start: 0.7982 (m-30) cc_final: 0.7721 (m-30)
REVERT: F   24 GLN cc_start: 0.8663 (mt0) cc_final: 0.8404 (mt0)
REVERT: F   75 LYS cc_start: 0.9434 (mmmt) cc_final: 0.8800 (tppt)
REVERT: H    8 ARG cc_start: 0.9271 (mmm-85) cc_final: 0.8996 (mmm-85)
REVERT: H  135 LYS cc_start: 0.9429 (tptp) cc_final: 0.9022 (ptpp)
REVERT: I    8 ARG cc_start: 0.9226 (mmm-85) cc_final: 0.8956 (mmm-85)
  outliers start: 22
  outliers final: 20
  residues processed: 159
  average time/residue: 0.1491
  time to fit residues: 29.9796
Evaluate side-chains
  159 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain E residue   35 THR
Chi-restraints excluded: chain E residue  105 ILE
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain F residue  117 ASP
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue    7 ASP
Chi-restraints excluded: chain G residue   35 THR
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue  105 ILE
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   35 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 22 optimal weight:    8.9990
   chunk 116 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 13 optimal weight:   10.0000
   chunk 40 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    9.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.040478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2557 r_free = 0.2557 target = 0.029591 restraints weight = 57885.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2599 r_free = 0.2599 target = 0.030579 restraints weight = 34944.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.031205 restraints weight = 25933.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.031578 restraints weight = 21707.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.031847 restraints weight = 19545.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start:          0.5435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9819  Z= 0.115
  Angle     :  0.588  12.671  13248  Z= 0.286
  Chirality :  0.037   0.126   1584
  Planarity :  0.004   0.028   1710
  Dihedral  :  2.884   9.628   1350
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.06 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.72 (0.24), residues: 1215
  helix:  3.46 (0.16), residues: 972
  sheet:  None (None), residues: 0
  loop :  1.65 (0.42), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A   8 
 TYR   0.004   0.000   TYR B  81 
 PHE   0.007   0.001   PHE F  73 
 HIS   0.001   0.000   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9819)
  covalent geometry    : angle       0.58794 (13248)
  hydrogen bonds       : bond        0.03042 (  702)
  hydrogen bonds       : angle       3.65116 ( 2106)

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 141
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 LYS cc_start: 0.9430 (mmmt) cc_final: 0.9188 (tppt)
REVERT: A  117 ASP cc_start: 0.8337 (t0) cc_final: 0.8075 (m-30)
REVERT: A  135 LYS cc_start: 0.9522 (tptp) cc_final: 0.9105 (ptpp)
REVERT: B    8 ARG cc_start: 0.9349 (mmm-85) cc_final: 0.9067 (mmm-85)
REVERT: B  135 LYS cc_start: 0.9479 (tptp) cc_final: 0.9026 (ptpp)
REVERT: E   75 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.9115 (tppt)
REVERT: F   24 GLN cc_start: 0.8672 (mt0) cc_final: 0.8430 (mt0)
REVERT: F   75 LYS cc_start: 0.9427 (mmmt) cc_final: 0.8791 (tppt)
REVERT: G  117 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7880 (m-30)
REVERT: H    8 ARG cc_start: 0.9299 (mmm-85) cc_final: 0.9011 (mmm-85)
REVERT: H  135 LYS cc_start: 0.9489 (tptp) cc_final: 0.9098 (ptpp)
REVERT: I    8 ARG cc_start: 0.9265 (mmm-85) cc_final: 0.8989 (mmm-85)
  outliers start: 27
  outliers final: 22
  residues processed: 157
  average time/residue: 0.1365
  time to fit residues: 27.1514
Evaluate side-chains
  160 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 VAL
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue  105 ILE
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain D residue   35 THR
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain E residue   35 THR
Chi-restraints excluded: chain E residue   55 SER
Chi-restraints excluded: chain E residue   75 LYS
Chi-restraints excluded: chain E residue  105 ILE
Chi-restraints excluded: chain F residue    3 VAL
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain F residue  117 ASP
Chi-restraints excluded: chain G residue    7 ASP
Chi-restraints excluded: chain G residue   35 THR
Chi-restraints excluded: chain G residue  117 ASP
Chi-restraints excluded: chain H residue    3 VAL
Chi-restraints excluded: chain H residue  105 ILE
Chi-restraints excluded: chain I residue    3 VAL
Chi-restraints excluded: chain I residue   35 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 15 optimal weight:    0.1980
   chunk 54 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 114 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 28 optimal weight:    0.4980
   chunk 104 optimal weight:   10.0000
   chunk 1 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0000
   overall best weight:    0.4184

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.040960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2582 r_free = 0.2582 target = 0.030181 restraints weight = 58057.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.031194 restraints weight = 34698.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.031829 restraints weight = 25623.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.032210 restraints weight = 21352.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.032495 restraints weight = 19188.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8826
moved from start:          0.5578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9819  Z= 0.108
  Angle     :  0.596  13.326  13248  Z= 0.287
  Chirality :  0.037   0.129   1584
  Planarity :  0.004   0.031   1710
  Dihedral  :  2.867   9.720   1350
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.06 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.92 (0.23), residues: 1215
  helix:  3.55 (0.16), residues: 963
  sheet:  None (None), residues: 0
  loop :  2.01 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G 108 
 TYR   0.003   0.000   TYR B  81 
 PHE   0.006   0.001   PHE H  73 
 HIS   0.002   0.000   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 9819)
  covalent geometry    : angle       0.59553 (13248)
  hydrogen bonds       : bond        0.02934 (  702)
  hydrogen bonds       : angle       3.65078 ( 2106)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1514.57 seconds
wall clock time: 26 minutes 48.00 seconds (1608.00 seconds total)