Starting phenix.real_space_refine
on Wed Mar  4 07:08:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cze_27096/03_2026/8cze_27096.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cze_27096/03_2026/8cze_27096.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cze_27096/03_2026/8cze_27096.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cze_27096/03_2026/8cze_27096.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cze_27096/03_2026/8cze_27096.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cze_27096/03_2026/8cze_27096.map"
  }
  resolution = 2.58
  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=   0.034
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     292      5.49       5
     S      12      5.16       5
     C    6646      2.51       5
     N    2258      2.21       5
     O    2821      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: 12029
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 841
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 801
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 841
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 3009
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3009
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "J"
      Number of atoms: 2977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 2977
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
  Time building chain proxies: 2.85, per 1000 atoms: 0.24
  Number of scatterers: 12029
  At special positions: 0
  Unit cell: (79.2, 118.8, 126.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     P     292     15.00
     O    2821      8.00
     N    2258      7.00
     C    6646      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Conformation dependent library (CDL) restraints added in 373.4 milliseconds
  

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1430

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 8 sheets defined
      72.1% alpha, 2.6% beta
      133 base pairs and 267 stacking pairs defined.
    Time for finding SS restraints: 1.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.520A  pdb=" N   LEU A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.845A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 4.352A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   MET A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.720A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
      removed outlier: 3.523A  pdb=" N   ILE B  34 " --> pdb=" O   THR B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.378A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.668A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 27 through 36
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.541A  pdb=" N   TYR C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.568A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
      removed outlier: 3.863A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.525A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 121
      removed outlier: 3.859A  pdb=" N   LYS D 105 " --> pdb=" O   GLY D 101 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA D 121 " --> pdb=" O   LYS D 117 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.520A  pdb=" N   LEU E  48 " --> pdb=" O   GLY E  44 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   SER E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.846A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 4.352A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   MET E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.719A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 3.523A  pdb=" N   ILE F  34 " --> pdb=" O   THR F  30 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.378A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.668A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 27 through 36
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.541A  pdb=" N   TYR G  50 " --> pdb=" O   GLY G  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.568A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 3.862A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
      removed outlier: 3.525A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 101 through 121
      removed outlier: 3.858A  pdb=" N   LYS H 105 " --> pdb=" O   GLY H 101 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA H 121 " --> pdb=" O   LYS H 117 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.989A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.511A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.717A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.385A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.008A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.557A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.417A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    374 hydrogen bonds defined for protein.
    1098 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      345 hydrogen bonds
      690 hydrogen bond angles
      0 basepair planarities
      133 basepair parallelities
      267 stacking parallelities
  Total time for adding SS restraints: 2.28

  Time building geometry restraints manager: 1.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2427
        1.34 -     1.45: 4063
        1.45 -     1.57: 5743
        1.57 -     1.69: 582
        1.69 -     1.81: 22
  Bond restraints: 12837
  Sorted by residual:
  bond pdb=" C3'  DC I  52 "
       pdb=" O3'  DC I  52 "
    ideal  model  delta    sigma   weight residual
    1.422  1.462 -0.040 3.00e-02 1.11e+03 1.81e+00
  bond pdb=" C   GLU C  61 "
       pdb=" O   GLU C  61 "
    ideal  model  delta    sigma   weight residual
    1.236  1.249 -0.013 1.15e-02 7.56e+03 1.23e+00
  bond pdb=" C   GLU G  61 "
       pdb=" O   GLU G  61 "
    ideal  model  delta    sigma   weight residual
    1.236  1.249 -0.012 1.15e-02 7.56e+03 1.15e+00
  bond pdb=" C3'  DC I  30 "
       pdb=" C2'  DC I  30 "
    ideal  model  delta    sigma   weight residual
    1.525  1.546 -0.021 2.00e-02 2.50e+03 1.08e+00
  bond pdb=" C3'  DC J  21 "
       pdb=" C2'  DC J  21 "
    ideal  model  delta    sigma   weight residual
    1.525  1.545 -0.020 2.00e-02 2.50e+03 1.01e+00
  ... (remaining 12832 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 17331
        1.03 -     2.05: 1005
        2.05 -     3.08: 243
        3.08 -     4.11: 8
        4.11 -     5.13: 8
  Bond angle restraints: 18595
  Sorted by residual:
  angle pdb=" C3'  DC I  52 "
        pdb=" O3'  DC I  52 "
        pdb=" P    DC I  53 "
      ideal   model   delta    sigma   weight residual
     120.20  123.32   -3.12 1.50e+00 4.44e-01 4.32e+00
  angle pdb=" N   LYS B  31 "
        pdb=" CA  LYS B  31 "
        pdb=" C   LYS B  31 "
      ideal   model   delta    sigma   weight residual
     109.81  114.04   -4.23 2.21e+00 2.05e-01 3.66e+00
  angle pdb=" N   LYS F  31 "
        pdb=" CA  LYS F  31 "
        pdb=" C   LYS F  31 "
      ideal   model   delta    sigma   weight residual
     109.81  114.01   -4.20 2.21e+00 2.05e-01 3.61e+00
  angle pdb=" O4'  DC I -25 "
        pdb=" C1'  DC I -25 "
        pdb=" C2'  DC I -25 "
      ideal   model   delta    sigma   weight residual
     106.40  103.60    2.80 1.50e+00 4.44e-01 3.49e+00
  angle pdb=" C3'  DC I -40 "
        pdb=" C2'  DC I -40 "
        pdb=" C1'  DC I -40 "
      ideal   model   delta    sigma   weight residual
     101.60  104.36   -2.76 1.50e+00 4.44e-01 3.38e+00
  ... (remaining 18590 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.85: 5600
       33.85 -    67.70: 1366
       67.70 -   101.55: 3
      101.55 -   135.40: 0
      135.40 -   169.24: 1
  Dihedral angle restraints: 6970
    sinusoidal: 4755
      harmonic: 2215
  Sorted by residual:
  dihedral pdb=" C4'  DC I  52 "
           pdb=" C3'  DC I  52 "
           pdb=" O3'  DC I  52 "
           pdb=" P    DC I  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   50.76  169.24     1      3.50e+01 8.16e-04 1.55e+01
  dihedral pdb=" CA  PRO H 100 "
           pdb=" C   PRO H 100 "
           pdb=" N   GLY H 101 "
           pdb=" CA  GLY H 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.25   14.75     0      5.00e+00 4.00e-02 8.70e+00
  dihedral pdb=" CA  PRO D 100 "
           pdb=" C   PRO D 100 "
           pdb=" N   GLY D 101 "
           pdb=" CA  GLY D 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.28   14.72     0      5.00e+00 4.00e-02 8.67e+00
  ... (remaining 6967 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1409
       0.026 -    0.052: 482
       0.052 -    0.079: 164
       0.079 -    0.105: 38
       0.105 -    0.131: 30
  Chirality restraints: 2123
  Sorted by residual:
  chirality pdb=" CA  ILE B  46 "
            pdb=" N   ILE B  46 "
            pdb=" C   ILE B  46 "
            pdb=" CB  ILE B  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.28e-01
  chirality pdb=" CA  ILE G  79 "
            pdb=" N   ILE G  79 "
            pdb=" C   ILE G  79 "
            pdb=" CB  ILE G  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  chirality pdb=" CA  ILE C  79 "
            pdb=" N   ILE C  79 "
            pdb=" C   ILE C  79 "
            pdb=" CB  ILE C  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.99e-01
  ... (remaining 2120 not shown)

  Planarity restraints: 1341
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J -49 "    0.025 2.00e-02 2.50e+03   1.06e-02 3.39e+00
        pdb=" N9   DG J -49 "   -0.026 2.00e-02 2.50e+03
        pdb=" C8   DG J -49 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7   DG J -49 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG J -49 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG J -49 "    0.002 2.00e-02 2.50e+03
        pdb=" O6   DG J -49 "    0.006 2.00e-02 2.50e+03
        pdb=" N1   DG J -49 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DG J -49 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2   DG J -49 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DG J -49 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DG J -49 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  47 "    0.022 2.00e-02 2.50e+03   9.85e-03 2.67e+00
        pdb=" N9   DA I  47 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8   DA I  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I  47 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DA I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" N6   DA I  47 "    0.008 2.00e-02 2.50e+03
        pdb=" N1   DA I  47 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DA I  47 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I -35 "   -0.022 2.00e-02 2.50e+03   9.05e-03 2.45e+00
        pdb=" N9   DG I -35 "    0.020 2.00e-02 2.50e+03
        pdb=" C8   DG I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I -35 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I -35 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1   DG I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DG I -35 "    0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DG I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I -35 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1338 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2335
        2.81 -     3.33: 9353
        3.33 -     3.85: 20452
        3.85 -     4.38: 25395
        4.38 -     4.90: 36571
  Nonbonded interactions: 94106
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH2 ARG E 131 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH2 ARG A 131 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" OD1 ASP C  90 "
            pdb=" N   GLU C  91 "
     model   vdw
     2.350 3.120
  nonbonded pdb=" OD1 ASP G  90 "
            pdb=" N   GLU G  91 "
     model   vdw
     2.351 3.120
  nonbonded pdb=" O   THR G  10 "
            pdb=" OG1 THR G  10 "
     model   vdw
     2.381 3.040
  ... (remaining 94101 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 38 through 133 or (resid 134 and (name N or name CA or nam \ 
e C or name O or name CB ))))
  selection = (chain 'E' and resid 38 through 134)
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.200
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  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:6.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
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      :  0.004   0.040  12837  Z= 0.174
  Angle     :  0.553   5.134  18595  Z= 0.339
  Chirality :  0.033   0.131   2123
  Planarity :  0.004   0.033   1341
  Dihedral  : 25.806 169.245   5540
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  4.42 %
    Favored  : 95.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.43 (0.31), residues: 747
  helix:  2.98 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -1.74 (0.34), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  39 
 TYR   0.009   0.001   TYR C  50 
 PHE   0.009   0.001   PHE F  61 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (12837)
  covalent geometry    : angle       0.55292 (18595)
  hydrogen bonds       : bond        0.10742 (  719)
  hydrogen bonds       : angle       3.10541 ( 1788)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 0.258 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7113 (t0)
REVERT: C   75 LYS cc_start: 0.8483 (mmtp) cc_final: 0.8183 (mmtp)
REVERT: C   99 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7910 (mtp85)
REVERT: D   31 LYS cc_start: 0.8645 (mttm) cc_final: 0.8353 (mtmm)
REVERT: D   59 MET cc_start: 0.9122 (mmp) cc_final: 0.8879 (mmm)
REVERT: D   65 ASP cc_start: 0.9239 (t0) cc_final: 0.8871 (t0)
REVERT: D   73 GLU cc_start: 0.9108 (tp30) cc_final: 0.8683 (tp30)
REVERT: E  105 GLU cc_start: 0.8015 (tt0) cc_final: 0.7738 (mt-10)
REVERT: F   74 GLU cc_start: 0.8251 (tt0) cc_final: 0.8015 (tt0)
REVERT: G   73 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.6892 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 119
  average time/residue: 0.9349
  time to fit residues: 116.7527
Evaluate side-chains
  101 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain G residue   73 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.9184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.091041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.069343 restraints weight = 20753.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 1.60
r_work: 0.2842 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.0613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12837  Z= 0.171
  Angle     :  0.543   5.263  18595  Z= 0.335
  Chirality :  0.033   0.132   2123
  Planarity :  0.004   0.034   1341
  Dihedral  : 29.051 169.075   4046
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.64 %
    Favored  : 89.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.66 (0.31), residues: 747
  helix:  3.14 (0.23), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.75 (0.35), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  96 
 TYR   0.008   0.001   TYR G  50 
 PHE   0.010   0.001   PHE F  61 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (12837)
  covalent geometry    : angle       0.54333 (18595)
  hydrogen bonds       : bond        0.06750 (  719)
  hydrogen bonds       : angle       2.64408 ( 1788)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.266 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7495 (t0) cc_final: 0.6915 (t0)
REVERT: C   99 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8109 (mtp85)
REVERT: D   59 MET cc_start: 0.8793 (mmp) cc_final: 0.8516 (mmm)
REVERT: D   65 ASP cc_start: 0.9001 (t0) cc_final: 0.8632 (t0)
REVERT: D   73 GLU cc_start: 0.9029 (tp30) cc_final: 0.8631 (tp30)
REVERT: E  105 GLU cc_start: 0.8098 (tt0) cc_final: 0.7724 (mt-10)
REVERT: F   74 GLU cc_start: 0.8363 (tt0) cc_final: 0.8113 (tt0)
  outliers start: 7
  outliers final: 6
  residues processed: 106
  average time/residue: 0.9269
  time to fit residues: 103.4161
Evaluate side-chains
  107 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   87 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 93 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 95 optimal weight:    6.9990
   chunk 86 optimal weight:   10.0000
   chunk 83 optimal weight:    6.9990
   overall best weight:    2.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.089311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.067236 restraints weight = 20805.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 1.59
r_work: 0.2790 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2662 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.0881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12837  Z= 0.214
  Angle     :  0.566   6.076  18595  Z= 0.346
  Chirality :  0.035   0.135   2123
  Planarity :  0.005   0.038   1341
  Dihedral  : 28.999 168.458   4042
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 10.27 %
    Favored  : 88.63 %
  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:  2.52 (0.31), residues: 747
  helix:  3.05 (0.23), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.83 (0.35), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  30 
 TYR   0.010   0.002   TYR G  50 
 PHE   0.014   0.002   PHE F  61 
 HIS   0.004   0.001   HIS D 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 (12837)
  covalent geometry    : angle       0.56576 (18595)
  hydrogen bonds       : bond        0.07722 (  719)
  hydrogen bonds       : angle       2.63063 ( 1788)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.322 
Fit side-chains
REVERT: C   73 ASN cc_start: 0.7470 (t0) cc_final: 0.6888 (t0)
REVERT: C   99 ARG cc_start: 0.8469 (mtp85) cc_final: 0.8125 (mtp85)
REVERT: D   59 MET cc_start: 0.8849 (mmp) cc_final: 0.8590 (mmm)
REVERT: D   65 ASP cc_start: 0.9083 (t0) cc_final: 0.8673 (t0)
REVERT: D   73 GLU cc_start: 0.9050 (tp30) cc_final: 0.8452 (tp30)
REVERT: E  105 GLU cc_start: 0.8143 (tt0) cc_final: 0.7882 (mt-10)
REVERT: F   74 GLU cc_start: 0.8492 (tt0) cc_final: 0.8258 (tt0)
  outliers start: 7
  outliers final: 6
  residues processed: 109
  average time/residue: 0.9418
  time to fit residues: 107.9238
Evaluate side-chains
  107 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   87 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0030
   chunk 64 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 97 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    1.3996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.089733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.067714 restraints weight = 20699.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 1.60
r_work: 0.2801 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2672 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.0891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12837  Z= 0.186
  Angle     :  0.553   6.638  18595  Z= 0.340
  Chirality :  0.034   0.128   2123
  Planarity :  0.004   0.037   1341
  Dihedral  : 29.004 168.526   4042
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 11.53 %
    Favored  : 87.52 %
  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:  2.52 (0.31), residues: 747
  helix:  3.05 (0.22), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.83 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  39 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.012   0.002   PHE F  61 
 HIS   0.002   0.001   HIS D 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (12837)
  covalent geometry    : angle       0.55251 (18595)
  hydrogen bonds       : bond        0.07453 (  719)
  hydrogen bonds       : angle       2.63121 ( 1788)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 103
  time to evaluate  : 0.333 
Fit side-chains
REVERT: C   72 ASP cc_start: 0.7694 (t0) cc_final: 0.7364 (m-30)
REVERT: C   73 ASN cc_start: 0.7416 (t0) cc_final: 0.6706 (t0)
REVERT: C   95 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8646 (ttpp)
REVERT: C   99 ARG cc_start: 0.8472 (mtp85) cc_final: 0.8126 (mtp85)
REVERT: D   59 MET cc_start: 0.8864 (mmp) cc_final: 0.8657 (mmm)
REVERT: D   65 ASP cc_start: 0.9079 (t0) cc_final: 0.8656 (t0)
REVERT: D   73 GLU cc_start: 0.9046 (tp30) cc_final: 0.8610 (tp30)
REVERT: E  105 GLU cc_start: 0.8127 (tt0) cc_final: 0.7873 (mt-10)
REVERT: F   74 GLU cc_start: 0.8482 (tt0) cc_final: 0.8255 (tt0)
  outliers start: 6
  outliers final: 5
  residues processed: 106
  average time/residue: 0.9720
  time to fit residues: 108.3151
Evaluate side-chains
  108 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   87 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 96 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    1.9586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.089769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.067795 restraints weight = 20680.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 1.59
r_work: 0.2806 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2678 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12837  Z= 0.205
  Angle     :  0.556   5.532  18595  Z= 0.341
  Chirality :  0.034   0.132   2123
  Planarity :  0.004   0.038   1341
  Dihedral  : 29.000 168.766   4042
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.74 %
    Favored  : 87.52 %
  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:  2.52 (0.31), residues: 747
  helix:  3.06 (0.22), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.86 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  30 
 TYR   0.009   0.001   TYR G  50 
 PHE   0.012   0.002   PHE F  61 
 HIS   0.003   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (12837)
  covalent geometry    : angle       0.55642 (18595)
  hydrogen bonds       : bond        0.07468 (  719)
  hydrogen bonds       : angle       2.58986 ( 1788)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.324 
Fit side-chains
REVERT: C   99 ARG cc_start: 0.8458 (mtp85) cc_final: 0.8067 (mtp85)
REVERT: D   59 MET cc_start: 0.8855 (mmp) cc_final: 0.8647 (mmm)
REVERT: D   65 ASP cc_start: 0.9077 (t0) cc_final: 0.8672 (t0)
REVERT: D   73 GLU cc_start: 0.9014 (tp30) cc_final: 0.8423 (tp30)
REVERT: D   82 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8845 (mtpt)
REVERT: E  105 GLU cc_start: 0.8139 (tt0) cc_final: 0.7929 (mt-10)
REVERT: F   74 GLU cc_start: 0.8497 (tt0) cc_final: 0.8248 (tt0)
REVERT: G   73 ASN cc_start: 0.7103 (t0) cc_final: 0.6739 (t0)
  outliers start: 11
  outliers final: 6
  residues processed: 108
  average time/residue: 0.9127
  time to fit residues: 103.6276
Evaluate side-chains
  106 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   87 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 98 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 96 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 89 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   overall best weight:    2.7786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.088000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.065780 restraints weight = 20592.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 1.60
r_work: 0.2762 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2632 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.1233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  12837  Z= 0.253
  Angle     :  0.598   6.995  18595  Z= 0.364
  Chirality :  0.037   0.144   2123
  Planarity :  0.005   0.040   1341
  Dihedral  : 29.012 168.922   4042
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 10.74 %
    Favored  : 87.68 %
  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:  2.26 (0.31), residues: 747
  helix:  2.88 (0.22), residues: 518
  sheet:  None (None), residues: 0
  loop : -2.01 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  30 
 TYR   0.011   0.002   TYR G  50 
 PHE   0.013   0.002   PHE F  61 
 HIS   0.003   0.001   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00564 (12837)
  covalent geometry    : angle       0.59758 (18595)
  hydrogen bonds       : bond        0.08718 (  719)
  hydrogen bonds       : angle       2.74159 ( 1788)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.305 
Fit side-chains
REVERT: C   99 ARG cc_start: 0.8488 (mtp85) cc_final: 0.8043 (mtp85)
REVERT: D   65 ASP cc_start: 0.9097 (t0) cc_final: 0.8792 (t0)
REVERT: D   73 GLU cc_start: 0.8981 (tp30) cc_final: 0.8441 (tp30)
REVERT: D   82 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8863 (mtpt)
REVERT: E  105 GLU cc_start: 0.8058 (tt0) cc_final: 0.7790 (mt-10)
REVERT: F   74 GLU cc_start: 0.8580 (tt0) cc_final: 0.8280 (mt-10)
REVERT: G   73 ASN cc_start: 0.7341 (t0) cc_final: 0.6928 (t0)
  outliers start: 10
  outliers final: 7
  residues processed: 108
  average time/residue: 0.9493
  time to fit residues: 107.5763
Evaluate side-chains
  109 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 74 optimal weight:    7.9990
   chunk 2 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 89 optimal weight:    6.9990
   chunk 63 optimal weight:    0.5980
   chunk 69 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 26 optimal weight:    0.3980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
F  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.090170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.068237 restraints weight = 20578.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 1.59
r_work: 0.2816 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2688 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.1165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12837  Z= 0.166
  Angle     :  0.551   6.079  18595  Z= 0.339
  Chirality :  0.033   0.123   2123
  Planarity :  0.004   0.038   1341
  Dihedral  : 28.994 169.948   4042
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 12.16 %
    Favored  : 86.41 %
  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:  2.49 (0.31), residues: 747
  helix:  3.05 (0.23), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.91 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  30 
 TYR   0.009   0.001   TYR F  51 
 PHE   0.009   0.001   PHE B  61 
 HIS   0.002   0.000   HIS D 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (12837)
  covalent geometry    : angle       0.55134 (18595)
  hydrogen bonds       : bond        0.07075 (  719)
  hydrogen bonds       : angle       2.62055 ( 1788)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.208 
Fit side-chains
REVERT: C   99 ARG cc_start: 0.8477 (mtp85) cc_final: 0.8085 (mtp85)
REVERT: D   65 ASP cc_start: 0.9057 (t0) cc_final: 0.8726 (t0)
REVERT: D   73 GLU cc_start: 0.8980 (tp30) cc_final: 0.8395 (tp30)
REVERT: D   82 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8863 (mtpt)
REVERT: D  109 SER cc_start: 0.8587 (OUTLIER) cc_final: 0.8314 (m)
REVERT: E  105 GLU cc_start: 0.8088 (tt0) cc_final: 0.7860 (mt-10)
REVERT: F   74 GLU cc_start: 0.8463 (tt0) cc_final: 0.8210 (tt0)
REVERT: G   73 ASN cc_start: 0.7008 (t0) cc_final: 0.6649 (t0)
  outliers start: 9
  outliers final: 5
  residues processed: 110
  average time/residue: 0.8998
  time to fit residues: 103.9925
Evaluate side-chains
  109 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   87 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 20 optimal weight:    0.0870
   chunk 32 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 72 optimal weight:   10.0000
   chunk 74 optimal weight:    7.9990
   chunk 65 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8960

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.090194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.068312 restraints weight = 20890.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 1.59
r_work: 0.2810 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2685 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12837  Z= 0.169
  Angle     :  0.545   7.227  18595  Z= 0.333
  Chirality :  0.033   0.124   2123
  Planarity :  0.004   0.040   1341
  Dihedral  : 28.981 169.239   4042
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 12.80 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.61 (0.31), residues: 747
  helix:  3.14 (0.23), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.86 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG H  30 
 TYR   0.007   0.001   TYR G  50 
 PHE   0.009   0.001   PHE F  61 
 HIS   0.003   0.001   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (12837)
  covalent geometry    : angle       0.54526 (18595)
  hydrogen bonds       : bond        0.06688 (  719)
  hydrogen bonds       : angle       2.50242 ( 1788)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.330 
Fit side-chains
REVERT: C   99 ARG cc_start: 0.8496 (mtp85) cc_final: 0.8097 (mtp85)
REVERT: D   65 ASP cc_start: 0.9046 (t0) cc_final: 0.8689 (t0)
REVERT: D   73 GLU cc_start: 0.9037 (tp30) cc_final: 0.8626 (tp30)
REVERT: D   82 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8864 (mtpt)
REVERT: E  105 GLU cc_start: 0.8111 (tt0) cc_final: 0.7905 (mt-10)
REVERT: F   74 GLU cc_start: 0.8462 (tt0) cc_final: 0.8236 (tt0)
REVERT: G   73 ASN cc_start: 0.6931 (t0) cc_final: 0.6616 (t0)
  outliers start: 9
  outliers final: 6
  residues processed: 103
  average time/residue: 0.9747
  time to fit residues: 105.3234
Evaluate side-chains
  104 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   87 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 88 optimal weight:    7.9990
   chunk 74 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 60 optimal weight:    0.5980
   chunk 96 optimal weight:    6.9990
   chunk 26 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.092009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.070373 restraints weight = 21062.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 1.60
r_work: 0.2852 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2728 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.1310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12837  Z= 0.164
  Angle     :  0.529   6.894  18595  Z= 0.323
  Chirality :  0.032   0.126   2123
  Planarity :  0.004   0.051   1341
  Dihedral  : 28.969 168.426   4042
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 13.27 %
    Favored  : 85.47 %
  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:  2.76 (0.31), residues: 747
  helix:  3.24 (0.23), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.81 (0.34), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H  30 
 TYR   0.007   0.001   TYR G  50 
 PHE   0.009   0.001   PHE B  61 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (12837)
  covalent geometry    : angle       0.52942 (18595)
  hydrogen bonds       : bond        0.05860 (  719)
  hydrogen bonds       : angle       2.35857 ( 1788)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.339 
Fit side-chains
REVERT: C   99 ARG cc_start: 0.8486 (mtp85) cc_final: 0.8115 (mtp85)
REVERT: D   65 ASP cc_start: 0.9004 (t0) cc_final: 0.8528 (t0)
REVERT: D   73 GLU cc_start: 0.9069 (tp30) cc_final: 0.8704 (tp30)
REVERT: E  105 GLU cc_start: 0.8101 (tt0) cc_final: 0.7718 (mt-10)
REVERT: F   74 GLU cc_start: 0.8369 (tt0) cc_final: 0.8131 (tt0)
  outliers start: 8
  outliers final: 5
  residues processed: 106
  average time/residue: 0.9370
  time to fit residues: 104.3858
Evaluate side-chains
  104 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 96 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 90 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 86 optimal weight:   10.0000
   chunk 97 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0870
   chunk 55 optimal weight:    0.1980
   chunk 83 optimal weight:    6.9990
   overall best weight:    1.2562

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.091391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.069672 restraints weight = 21107.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.59
r_work: 0.2838 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2713 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12837  Z= 0.172
  Angle     :  0.535   7.629  18595  Z= 0.326
  Chirality :  0.032   0.129   2123
  Planarity :  0.004   0.041   1341
  Dihedral  : 28.964 168.517   4042
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 14.38 %
    Favored  : 84.83 %
  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:  2.75 (0.31), residues: 747
  helix:  3.22 (0.22), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.79 (0.34), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  30 
 TYR   0.008   0.001   TYR G  50 
 PHE   0.010   0.001   PHE F  61 
 HIS   0.003   0.001   HIS D 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (12837)
  covalent geometry    : angle       0.53514 (18595)
  hydrogen bonds       : bond        0.06207 (  719)
  hydrogen bonds       : angle       2.39059 ( 1788)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.333 
Fit side-chains
REVERT: B   84 MET cc_start: 0.9042 (mmp) cc_final: 0.8292 (mmp)
REVERT: C   99 ARG cc_start: 0.8514 (mtp85) cc_final: 0.8139 (mtp85)
REVERT: D   65 ASP cc_start: 0.9071 (t0) cc_final: 0.8620 (t0)
REVERT: D   73 GLU cc_start: 0.9109 (tp30) cc_final: 0.8746 (tp30)
REVERT: E  105 GLU cc_start: 0.8156 (tt0) cc_final: 0.7892 (mt-10)
REVERT: F   74 GLU cc_start: 0.8434 (tt0) cc_final: 0.8190 (tt0)
  outliers start: 5
  outliers final: 5
  residues processed: 102
  average time/residue: 0.9712
  time to fit residues: 103.9341
Evaluate side-chains
  104 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   48 ASP
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain E residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 85 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.087819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.065585 restraints weight = 20903.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.2927 rms_B_bonded: 1.58
r_work: 0.2748 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2621 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.1323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12837  Z= 0.242
  Angle     :  0.596   7.657  18595  Z= 0.359
  Chirality :  0.036   0.144   2123
  Planarity :  0.005   0.040   1341
  Dihedral  : 28.988 168.657   4042
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 14.22 %
    Favored  : 84.99 %
  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:  2.42 (0.31), residues: 747
  helix:  3.00 (0.22), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.93 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  30 
 TYR   0.010   0.002   TYR E  54 
 PHE   0.013   0.002   PHE F  61 
 HIS   0.003   0.001   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00539 (12837)
  covalent geometry    : angle       0.59565 (18595)
  hydrogen bonds       : bond        0.08382 (  719)
  hydrogen bonds       : angle       2.65831 ( 1788)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4229.71 seconds
wall clock time: 72 minutes 22.56 seconds (4342.56 seconds total)