Starting phenix.real_space_refine
on Fri Jul  3 04:18:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jl9_36389/07_2026/8jl9_36389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jl9_36389/07_2026/8jl9_36389.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jl9_36389/07_2026/8jl9_36389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jl9_36389/07_2026/8jl9_36389.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jl9_36389/07_2026/8jl9_36389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jl9_36389/07_2026/8jl9_36389.map"
  }
  resolution = 2.65
  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=   0.002 sd=   0.033
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     310      5.49       5
     S      14      5.16       5
     C    6763      2.51       5
     N    2312      2.21       5
     O    2915      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12314
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 831
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 783
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "F"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "G"
      Number of atoms: 831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 831
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "I"
      Number of atoms: 3178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 3178
          Classifications: {'DNA': 155}
          Link IDs: {'rna3p': 154}
    Chain: "J"
      Number of atoms: 3177
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 3177
          Classifications: {'DNA': 155}
          Link IDs: {'rna3p': 154}
  Time building chain proxies: 2.27, per 1000 atoms: 0.18
  Number of scatterers: 12314
  At special positions: 0
  Unit cell: (74.2, 120.84, 129.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     310     15.00
     O    2915      8.00
     N    2312      7.00
     C    6763      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: 0.99
  Conformation dependent library (CDL) restraints added in 302.0 milliseconds
  

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1398

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      73.4% alpha, 3.2% beta
      155 base pairs and 283 stacking pairs defined.
    Time for finding SS restraints: 1.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.932A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.656A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.481A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
      removed outlier: 3.504A  pdb=" N   LEU C 116 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 123
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.973A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.671A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.474A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 123
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.897A  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
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.277A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
      removed outlier: 6.329A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.914A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.126A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    412 hydrogen bonds defined for protein.
    1212 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      398 hydrogen bonds
      796 hydrogen bond angles
      0 basepair planarities
      155 basepair parallelities
      283 stacking parallelities
  Total time for adding SS restraints: 1.89

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2146
        1.33 -     1.45: 4427
        1.45 -     1.57: 5950
        1.57 -     1.69: 619
        1.69 -     1.81: 24
  Bond restraints: 13166
  Sorted by residual:
  bond pdb=" C   SER D  32 "
       pdb=" N   ARG D  33 "
    ideal  model  delta    sigma   weight residual
    1.330  1.257  0.073 1.39e-02 5.18e+03 2.73e+01
  bond pdb=" C3'  DT I -71 "
       pdb=" C2'  DT I -71 "
    ideal  model  delta    sigma   weight residual
    1.516  1.549 -0.033 8.00e-03 1.56e+04 1.73e+01
  bond pdb=" C3'  DT I -76 "
       pdb=" C2'  DT I -76 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 8.00e-03 1.56e+04 1.55e+01
  bond pdb=" C3'  DG I  77 "
       pdb=" C2'  DG I  77 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 8.00e-03 1.56e+04 1.54e+01
  bond pdb=" C3'  DC I -63 "
       pdb=" C2'  DC I -63 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 8.00e-03 1.56e+04 1.43e+01
  ... (remaining 13161 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 18078
        2.25 -     4.50: 964
        4.50 -     6.75: 68
        6.75 -     9.00: 1
        9.00 -    11.25: 1
  Bond angle restraints: 19112
  Sorted by residual:
  angle pdb=" O4'  DA J  71 "
        pdb=" C1'  DA J  71 "
        pdb=" N9   DA J  71 "
      ideal   model   delta    sigma   weight residual
     108.00  112.55   -4.55 7.00e-01 2.04e+00 4.22e+01
  angle pdb=" O4'  DA I  71 "
        pdb=" C1'  DA I  71 "
        pdb=" N9   DA I  71 "
      ideal   model   delta    sigma   weight residual
     108.00  112.08   -4.08 7.00e-01 2.04e+00 3.39e+01
  angle pdb=" O4'  DA J  16 "
        pdb=" C1'  DA J  16 "
        pdb=" N9   DA J  16 "
      ideal   model   delta    sigma   weight residual
     108.00  112.05   -4.05 7.00e-01 2.04e+00 3.35e+01
  angle pdb=" C   SER D  32 "
        pdb=" CA  SER D  32 "
        pdb=" CB  SER D  32 "
      ideal   model   delta    sigma   weight residual
     110.42  121.67  -11.25 1.99e+00 2.53e-01 3.20e+01
  angle pdb=" O4'  DT I -76 "
        pdb=" C1'  DT I -76 "
        pdb=" N1   DT I -76 "
      ideal   model   delta    sigma   weight residual
     108.00  104.14    3.86 7.00e-01 2.04e+00 3.04e+01
  ... (remaining 19107 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.16: 5357
       32.16 -    64.31: 1688
       64.31 -    96.47: 53
       96.47 -   128.63: 0
      128.63 -   160.79: 2
  Dihedral angle restraints: 7100
    sinusoidal: 4927
      harmonic: 2173
  Sorted by residual:
  dihedral pdb=" C   SER D  32 "
           pdb=" N   SER D  32 "
           pdb=" CA  SER D  32 "
           pdb=" CB  SER D  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.37   17.77     0      2.50e+00 1.60e-01 5.05e+01
  dihedral pdb=" N   SER D  32 "
           pdb=" C   SER D  32 "
           pdb=" CA  SER D  32 "
           pdb=" CB  SER D  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.82  -13.02     0      2.50e+00 1.60e-01 2.71e+01
  dihedral pdb=" CA  ARG D  33 "
           pdb=" C   ARG D  33 "
           pdb=" N   LYS D  34 "
           pdb=" CA  LYS D  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.72   20.28     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 7097 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.119: 1994
       0.119 -    0.238: 170
       0.238 -    0.357: 6
       0.357 -    0.476: 0
       0.476 -    0.595: 1
  Chirality restraints: 2171
  Sorted by residual:
  chirality pdb=" CA  SER D  32 "
            pdb=" N   SER D  32 "
            pdb=" C   SER D  32 "
            pdb=" CB  SER D  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.92    0.60 2.00e-01 2.50e+01 8.86e+00
  chirality pdb=" CA  PRO B  32 "
            pdb=" N   PRO B  32 "
            pdb=" C   PRO B  32 "
            pdb=" CB  PRO B  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.39    0.32 2.00e-01 2.50e+01 2.62e+00
  chirality pdb=" CA  PRO F  32 "
            pdb=" N   PRO F  32 "
            pdb=" C   PRO F  32 "
            pdb=" CB  PRO F  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.40    0.31 2.00e-01 2.50e+01 2.46e+00
  ... (remaining 2168 not shown)

  Planarity restraints: 1347
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  40 "   -0.099 2.00e-02 2.50e+03   5.09e-02 5.18e+01
        pdb=" CG  TYR D  40 "    0.052 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  40 "    0.033 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  40 "    0.057 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  40 "    0.023 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  40 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  40 "   -0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR D  40 "   -0.056 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  17 "   -0.531 9.50e-02 1.11e+02   2.38e-01 3.48e+01
        pdb=" NE  ARG G  17 "    0.032 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  17 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  17 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  17 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I -76 "    0.052 2.00e-02 2.50e+03   2.80e-02 1.96e+01
        pdb=" N1   DT I -76 "   -0.070 2.00e-02 2.50e+03
        pdb=" C2   DT I -76 "    0.002 2.00e-02 2.50e+03
        pdb=" O2   DT I -76 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DT I -76 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DT I -76 "    0.008 2.00e-02 2.50e+03
        pdb=" O4   DT I -76 "    0.012 2.00e-02 2.50e+03
        pdb=" C5   DT I -76 "   -0.000 2.00e-02 2.50e+03
        pdb=" C7   DT I -76 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DT I -76 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1344 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.47: 8
        2.47 -     3.08: 7511
        3.08 -     3.69: 20503
        3.69 -     4.29: 32533
        4.29 -     4.90: 46271
  Nonbonded interactions: 106826
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP F  68 "
            pdb=" NH1 ARG F  92 "
     model   vdw
     1.865 3.120
  nonbonded pdb=" NH2 ARG F  92 "
            pdb=" O   LEU H 100 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" O   HIS F  75 "
            pdb=" NH1 ARG H  92 "
     model   vdw
     2.399 3.120
  nonbonded pdb=" OH  TYR E  99 "
            pdb=" OE1 GLU E 133 "
     model   vdw
     2.403 3.040
  nonbonded pdb=" O   ASN D  67 "
            pdb=" OE1 GLU D  71 "
     model   vdw
     2.403 3.040
  ... (remaining 106821 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 39 through 133)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'I' and (resid -77 through -1 or resid 1 through 77))
  selection = (chain 'J' and (resid -77 through -1 or resid 1 through 77))
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.370
  Find NCS groups from input model:        0.140
  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:             0.010
  Load rotamer database and sin/cos tables:5.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6497
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   0.111  13166  Z= 0.595
  Angle     :  0.990  11.254  19112  Z= 0.817
  Chirality :  0.063   0.595   2171
  Planarity :  0.012   0.238   1347
  Dihedral  : 28.861 160.785   5702
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.16 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.14 %
  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:  0.24 (0.27), residues: 737
  helix:  0.48 (0.20), residues: 532
  sheet:  None (None), residues: 0
  loop : -0.40 (0.37), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  63 
 TYR   0.099   0.004   TYR D  40 
 PHE   0.012   0.002   PHE A  84 
 HIS   0.006   0.001   HIS H 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00713 /  0.59 (13166)
  covalent geometry    : angle       0.98959 /  0.82 (19112)
  hydrogen bonds       : bond        0.10462 /  7.13 (  810)
  hydrogen bonds       : angle       4.26159 /  3.14 ( 2008)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.7254 (mt) cc_final: 0.7029 (mt)
REVERT: A  106 ASP cc_start: 0.6034 (m-30) cc_final: 0.5524 (m-30)
REVERT: A  120 MET cc_start: 0.6701 (mtt) cc_final: 0.6388 (mtm)
REVERT: A  123 ASP cc_start: 0.6922 (m-30) cc_final: 0.6526 (m-30)
REVERT: A  128 ARG cc_start: 0.6531 (mtp180) cc_final: 0.6273 (mmm160)
REVERT: B   79 LYS cc_start: 0.6802 (mmtm) cc_final: 0.6554 (mmtp)
REVERT: B   84 MET cc_start: 0.6224 (mmm) cc_final: 0.5991 (mmp)
REVERT: C  104 GLN cc_start: 0.7350 (tp40) cc_final: 0.6913 (mp10)
REVERT: E   53 ARG cc_start: 0.6337 (ttp-110) cc_final: 0.5974 (ttp-110)
REVERT: E  120 MET cc_start: 0.6824 (mtt) cc_final: 0.6491 (mtm)
REVERT: E  122 LYS cc_start: 0.6425 (pttt) cc_final: 0.6153 (pttp)
REVERT: G   40 SER cc_start: 0.7793 (p) cc_final: 0.7524 (p)
REVERT: G   42 ARG cc_start: 0.5862 (mtp85) cc_final: 0.5392 (mtp85)
REVERT: G   89 ASN cc_start: 0.7383 (m-40) cc_final: 0.6977 (m110)
REVERT: H   71 GLU cc_start: 0.6421 (pt0) cc_final: 0.6035 (pt0)
REVERT: H  108 LYS cc_start: 0.7308 (tttp) cc_final: 0.7021 (ttpp)
  outliers start: 0
  outliers final: 1
  residues processed: 146
  average time/residue: 0.8827
  time to fit residues: 136.0006
Evaluate side-chains
  128 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  101 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 125 GLN
F  25 ASN
F  27 GLN
F  93 GLN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.120297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.104765 restraints weight = 16284.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 0.82
r_work: 0.3220 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  13166  Z= 0.155
  Angle     :  0.649   6.091  19112  Z= 0.385
  Chirality :  0.048   0.203   2171
  Planarity :  0.004   0.032   1347
  Dihedral  : 31.008 170.156   4225
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 17.50 %
    Favored  : 81.38 %
  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:  2.61 (0.30), residues: 737
  helix:  2.42 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.31 (0.39), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  71 
 TYR   0.018   0.001   TYR H  40 
 PHE   0.006   0.001   PHE A  67 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.15 (13166)
  covalent geometry    : angle       0.64915 /  0.39 (19112)
  hydrogen bonds       : bond        0.05354 /  3.58 (  810)
  hydrogen bonds       : angle       3.00142 /  2.26 ( 2008)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 132
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8302 (mtp-110) cc_final: 0.7924 (mtp85)
REVERT: A   83 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.6396 (mtm180)
REVERT: A  106 ASP cc_start: 0.7578 (m-30) cc_final: 0.7351 (m-30)
REVERT: D   71 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7313 (mt-10)
REVERT: F   84 MET cc_start: 0.8261 (mmm) cc_final: 0.7850 (tpp)
REVERT: G   62 ILE cc_start: 0.8187 (mm) cc_final: 0.7968 (OUTLIER)
REVERT: G   89 ASN cc_start: 0.8562 (m-40) cc_final: 0.8296 (m110)
  outliers start: 7
  outliers final: 1
  residues processed: 135
  average time/residue: 0.9070
  time to fit residues: 129.2071
Evaluate side-chains
  122 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 120
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain D residue   71 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 96 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 93 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 77 optimal weight:    7.9990
   chunk 82 optimal weight:    7.9990
   chunk 71 optimal weight:   10.0000
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN
F  25 ASN
F  27 GLN
G  73 ASN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.117153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.102137 restraints weight = 16694.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 0.76
r_work: 0.3180 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13166  Z= 0.150
  Angle     :  0.610   5.843  19112  Z= 0.370
  Chirality :  0.047   0.252   2171
  Planarity :  0.004   0.035   1347
  Dihedral  : 30.916 171.883   4223
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 19.10 %
    Favored  : 78.49 %
  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:  3.20 (0.30), residues: 737
  helix:  2.89 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.23 (0.38), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  71 
 TYR   0.013   0.002   TYR D  40 
 PHE   0.008   0.001   PHE A  67 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.15 (13166)
  covalent geometry    : angle       0.61030 /  0.37 (19112)
  hydrogen bonds       : bond        0.05182 /  3.46 (  810)
  hydrogen bonds       : angle       2.81168 /  2.13 ( 2008)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8316 (mtp-110) cc_final: 0.7914 (mtp85)
REVERT: A   63 ARG cc_start: 0.8270 (mmp80) cc_final: 0.8019 (mmt-90)
REVERT: A   83 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.6515 (mtm180)
REVERT: A  106 ASP cc_start: 0.7564 (m-30) cc_final: 0.7278 (m-30)
REVERT: A  128 ARG cc_start: 0.8668 (mtp180) cc_final: 0.8354 (mmm160)
REVERT: C   74 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8054 (mtmm)
REVERT: D   71 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7307 (mt-10)
REVERT: F   84 MET cc_start: 0.8254 (mmm) cc_final: 0.7884 (tpp)
REVERT: G   73 ASN cc_start: 0.7822 (t0) cc_final: 0.7476 (t160)
REVERT: G   89 ASN cc_start: 0.8567 (m-40) cc_final: 0.8325 (m110)
REVERT: H   78 SER cc_start: 0.8735 (t) cc_final: 0.8520 (p)
REVERT: H   79 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7767 (mtt180)
  outliers start: 15
  outliers final: 2
  residues processed: 127
  average time/residue: 0.9924
  time to fit residues: 132.5211
Evaluate side-chains
  124 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 118
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain H residue   79 ARG
Chi-restraints excluded: chain H residue  123 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 95 optimal weight:    8.9990
   chunk 46 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 87 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 4 optimal weight:    0.1980
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  39 HIS
B  93 GLN
C  73 ASN
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.118131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.102156 restraints weight = 16146.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 0.84
r_work: 0.3177 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  13166  Z= 0.142
  Angle     :  0.603   5.479  19112  Z= 0.361
  Chirality :  0.046   0.230   2171
  Planarity :  0.004   0.052   1347
  Dihedral  : 30.901 172.968   4223
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 19.58 %
    Favored  : 78.81 %
  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:  3.28 (0.30), residues: 737
  helix:  2.95 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.21 (0.39), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  36 
 TYR   0.011   0.001   TYR H  40 
 PHE   0.005   0.001   PHE A  67 
 HIS   0.002   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00233 /  0.14 (13166)
  covalent geometry    : angle       0.60281 /  0.36 (19112)
  hydrogen bonds       : bond        0.04808 /  3.21 (  810)
  hydrogen bonds       : angle       2.73409 /  2.06 ( 2008)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8339 (mtp-110) cc_final: 0.8089 (mtt-85)
REVERT: A   63 ARG cc_start: 0.8265 (mmp80) cc_final: 0.7881 (mmt-90)
REVERT: A   83 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.6431 (mtm180)
REVERT: A  106 ASP cc_start: 0.7607 (m-30) cc_final: 0.7344 (m-30)
REVERT: D   71 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7328 (mt-10)
REVERT: G   73 ASN cc_start: 0.7867 (t0) cc_final: 0.7466 (t160)
REVERT: G   91 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5418 (tp30)
REVERT: H   78 SER cc_start: 0.8734 (t) cc_final: 0.8510 (p)
REVERT: H   79 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7796 (mtt180)
  outliers start: 10
  outliers final: 2
  residues processed: 121
  average time/residue: 1.0005
  time to fit residues: 127.2765
Evaluate side-chains
  120 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 114
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   55 SER
Chi-restraints excluded: chain H residue   79 ARG
Chi-restraints excluded: chain H residue  123 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 68 optimal weight:    0.1980
   chunk 73 optimal weight:    7.9990
   chunk 54 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 44 optimal weight:    0.5980
   chunk 86 optimal weight:    9.9990
   chunk 41 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.116552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.100652 restraints weight = 16128.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 0.84
r_work: 0.3150 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13166  Z= 0.160
  Angle     :  0.614   6.712  19112  Z= 0.365
  Chirality :  0.047   0.235   2171
  Planarity :  0.004   0.038   1347
  Dihedral  : 30.865 174.023   4223
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 18.94 %
    Favored  : 78.81 %
  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:  3.19 (0.30), residues: 737
  helix:  2.88 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.20 (0.38), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  92 
 TYR   0.019   0.002   TYR F  88 
 PHE   0.014   0.001   PHE D  70 
 HIS   0.004   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.16 (13166)
  covalent geometry    : angle       0.61380 /  0.36 (19112)
  hydrogen bonds       : bond        0.05000 /  3.34 (  810)
  hydrogen bonds       : angle       2.72189 /  2.04 ( 2008)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8334 (mtp-110) cc_final: 0.8094 (mtt-85)
REVERT: A   63 ARG cc_start: 0.8324 (mmp80) cc_final: 0.7853 (mmt-90)
REVERT: A   83 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.6549 (mtm180)
REVERT: A  106 ASP cc_start: 0.7593 (m-30) cc_final: 0.7351 (m-30)
REVERT: C   74 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8101 (mtmm)
REVERT: D   71 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7063 (mp0)
REVERT: G   42 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7861 (mtt-85)
REVERT: G   73 ASN cc_start: 0.8023 (t0) cc_final: 0.7591 (t160)
REVERT: G   91 GLU cc_start: 0.6365 (OUTLIER) cc_final: 0.5340 (tp30)
REVERT: H   78 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8496 (p)
REVERT: H   79 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7777 (mtt90)
REVERT: H   93 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7044 (mp0)
  outliers start: 14
  outliers final: 2
  residues processed: 116
  average time/residue: 0.9671
  time to fit residues: 118.2046
Evaluate side-chains
  116 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue   79 ARG
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain H residue  123 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 82 optimal weight:    7.9990
   chunk 29 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0370
   chunk 40 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0980
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.5058

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 125 GLN
B  93 GLN
C  73 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.117148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.101360 restraints weight = 16025.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 0.82
r_work: 0.3151 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  13166  Z= 0.137
  Angle     :  0.604   6.644  19112  Z= 0.360
  Chirality :  0.045   0.228   2171
  Planarity :  0.004   0.038   1347
  Dihedral  : 30.871 174.376   4223
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 19.90 %
    Favored  : 78.01 %
  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:  3.24 (0.30), residues: 737
  helix:  2.92 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.22 (0.38), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 129 
 TYR   0.011   0.001   TYR F  88 
 PHE   0.007   0.001   PHE D  70 
 HIS   0.002   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00221 /  0.14 (13166)
  covalent geometry    : angle       0.60437 /  0.36 (19112)
  hydrogen bonds       : bond        0.04823 /  3.22 (  810)
  hydrogen bonds       : angle       2.71972 /  2.04 ( 2008)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8336 (mtp-110) cc_final: 0.8111 (mtt-85)
REVERT: A   63 ARG cc_start: 0.8297 (mmp80) cc_final: 0.7836 (mmt-90)
REVERT: A   83 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.6503 (mtm180)
REVERT: A  106 ASP cc_start: 0.7593 (m-30) cc_final: 0.7331 (m-30)
REVERT: B   95 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7442 (mtt-85)
REVERT: D   71 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7042 (mp0)
REVERT: G   73 ASN cc_start: 0.8018 (t0) cc_final: 0.7600 (t160)
REVERT: G   91 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.5315 (tp30)
REVERT: H   59 MET cc_start: 0.8716 (tpt) cc_final: 0.8129 (tpt)
REVERT: H   78 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8498 (p)
REVERT: H   79 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7764 (mtt90)
REVERT: H   93 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7030 (mp0)
  outliers start: 13
  outliers final: 2
  residues processed: 107
  average time/residue: 1.0750
  time to fit residues: 120.4258
Evaluate side-chains
  110 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue   79 ARG
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 89 optimal weight:    6.9990
   chunk 76 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 44 optimal weight:    0.3980
   chunk 17 optimal weight:    0.3980
   chunk 21 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.6182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN
C  73 ASN
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.117718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.101949 restraints weight = 15909.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 0.82
r_work: 0.3159 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  13166  Z= 0.139
  Angle     :  0.594   6.862  19112  Z= 0.356
  Chirality :  0.045   0.229   2171
  Planarity :  0.004   0.038   1347
  Dihedral  : 30.872 175.096   4223
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 20.39 %
    Favored  : 77.85 %
  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:  3.24 (0.30), residues: 737
  helix:  2.91 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.19 (0.38), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  52 
 TYR   0.008   0.001   TYR H  40 
 PHE   0.007   0.001   PHE D  70 
 HIS   0.002   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00229 /  0.14 (13166)
  covalent geometry    : angle       0.59432 /  0.36 (19112)
  hydrogen bonds       : bond        0.04710 /  3.15 (  810)
  hydrogen bonds       : angle       2.69731 /  2.03 ( 2008)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8341 (mtp-110) cc_final: 0.8118 (mtt-85)
REVERT: A   63 ARG cc_start: 0.8280 (mmp80) cc_final: 0.7818 (mmt-90)
REVERT: A   83 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.6511 (mtm180)
REVERT: A  106 ASP cc_start: 0.7576 (m-30) cc_final: 0.7324 (m-30)
REVERT: B   95 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7459 (mtt-85)
REVERT: D   71 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7048 (mp0)
REVERT: G   73 ASN cc_start: 0.8013 (t0) cc_final: 0.7601 (t160)
REVERT: G   91 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5315 (tp30)
REVERT: H   59 MET cc_start: 0.8727 (tpt) cc_final: 0.7975 (tpt)
REVERT: H   78 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.8493 (p)
REVERT: H   79 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7734 (mtt90)
REVERT: H   93 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7036 (mp0)
  outliers start: 11
  outliers final: 2
  residues processed: 107
  average time/residue: 1.0473
  time to fit residues: 117.6344
Evaluate side-chains
  108 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain G residue   40 SER
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue   79 ARG
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 82 optimal weight:    7.9990
   chunk 70 optimal weight:   20.0000
   chunk 92 optimal weight:    6.9990
   chunk 71 optimal weight:   10.0000
   chunk 76 optimal weight:    8.9990
   chunk 35 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0570
   chunk 27 optimal weight:    0.9980
   chunk 84 optimal weight:   10.0000
   overall best weight:    1.6104

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
B  93 GLN
C  73 ASN
D  84 ASN
E  68 GLN
F  75 HIS
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.113126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.097182 restraints weight = 15972.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 0.82
r_work: 0.3090 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  13166  Z= 0.224
  Angle     :  0.668   6.653  19112  Z= 0.387
  Chirality :  0.051   0.240   2171
  Planarity :  0.005   0.042   1347
  Dihedral  : 30.830 175.394   4223
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 20.55 %
    Favored  : 77.85 %
  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:  2.88 (0.30), residues: 737
  helix:  2.66 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.37 (0.38), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  55 
 TYR   0.015   0.002   TYR D  40 
 PHE   0.010   0.002   PHE D  70 
 HIS   0.005   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00466 /  0.22 (13166)
  covalent geometry    : angle       0.66765 /  0.39 (19112)
  hydrogen bonds       : bond        0.05771 /  3.87 (  810)
  hydrogen bonds       : angle       2.81714 /  2.11 ( 2008)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8355 (mtp-110) cc_final: 0.8138 (mtt-85)
REVERT: A   42 ARG cc_start: 0.7906 (mtt90) cc_final: 0.7671 (mtt90)
REVERT: A   63 ARG cc_start: 0.8381 (mmp80) cc_final: 0.7859 (mmt-90)
REVERT: A   83 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.6763 (mtm180)
REVERT: A  106 ASP cc_start: 0.7630 (m-30) cc_final: 0.7391 (m-30)
REVERT: B   95 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7422 (mtp-110)
REVERT: D   62 MET cc_start: 0.8574 (mmp) cc_final: 0.8356 (mmt)
REVERT: D   71 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7111 (mp0)
REVERT: E   40 ARG cc_start: 0.8283 (mmm160) cc_final: 0.8066 (mtp180)
REVERT: E  133 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6869 (mt-10)
REVERT: G   73 ASN cc_start: 0.8150 (t0) cc_final: 0.7731 (t160)
REVERT: G   91 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5099 (tp30)
REVERT: H   93 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7090 (mp0)
  outliers start: 10
  outliers final: 1
  residues processed: 100
  average time/residue: 1.1133
  time to fit residues: 116.5615
Evaluate side-chains
  97 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 94 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 82 optimal weight:    7.9990
   chunk 84 optimal weight:    9.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 125 GLN
B  93 GLN
C  73 ASN
F  27 GLN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.113939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.097987 restraints weight = 15917.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 0.82
r_work: 0.3100 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13166  Z= 0.158
  Angle     :  0.651   9.465  19112  Z= 0.379
  Chirality :  0.049   0.236   2171
  Planarity :  0.004   0.041   1347
  Dihedral  : 30.853 175.409   4223
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 20.22 %
    Favored  : 78.33 %
  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:  2.98 (0.30), residues: 737
  helix:  2.74 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.33 (0.38), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  52 
 TYR   0.013   0.002   TYR D  40 
 PHE   0.007   0.001   PHE D  70 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.16 (13166)
  covalent geometry    : angle       0.65067 /  0.38 (19112)
  hydrogen bonds       : bond        0.05394 /  3.62 (  810)
  hydrogen bonds       : angle       2.81357 /  2.12 ( 2008)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8351 (mtp-110) cc_final: 0.8135 (mtt-85)
REVERT: A   42 ARG cc_start: 0.7896 (mtt90) cc_final: 0.7660 (mtt90)
REVERT: A   63 ARG cc_start: 0.8369 (mmp80) cc_final: 0.7851 (mmt-90)
REVERT: A   83 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.6751 (mtm180)
REVERT: A  106 ASP cc_start: 0.7647 (m-30) cc_final: 0.7410 (m-30)
REVERT: B   95 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7509 (mtt-85)
REVERT: D   62 MET cc_start: 0.8565 (mmp) cc_final: 0.8336 (mmt)
REVERT: D   71 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7066 (mp0)
REVERT: E  133 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6876 (mt-10)
REVERT: G   73 ASN cc_start: 0.8122 (t0) cc_final: 0.7710 (t160)
REVERT: G   91 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.5067 (tp30)
REVERT: H   93 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7089 (mp0)
  outliers start: 9
  outliers final: 1
  residues processed: 97
  average time/residue: 1.0919
  time to fit residues: 110.9978
Evaluate side-chains
  98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    8.9990
   chunk 74 optimal weight:    7.9990
   chunk 49 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 19 optimal weight:    0.0870
   chunk 50 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 97 optimal weight:    6.9990
   chunk 75 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    1.1762

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 125 GLN
B  93 GLN
C  73 ASN
D  84 ASN
F  27 GLN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.113866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.097993 restraints weight = 16075.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 0.82
r_work: 0.3100 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  13166  Z= 0.185
  Angle     :  0.649   7.044  19112  Z= 0.378
  Chirality :  0.049   0.235   2171
  Planarity :  0.004   0.041   1347
  Dihedral  : 30.857 176.025   4223
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 20.06 %
    Favored  : 78.33 %
  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:  2.92 (0.30), residues: 737
  helix:  2.69 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.35 (0.38), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  52 
 TYR   0.013   0.002   TYR D  40 
 PHE   0.007   0.001   PHE D  70 
 HIS   0.004   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.18 (13166)
  covalent geometry    : angle       0.64905 /  0.38 (19112)
  hydrogen bonds       : bond        0.05440 /  3.65 (  810)
  hydrogen bonds       : angle       2.78855 /  2.10 ( 2008)

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7887 (mtt90) cc_final: 0.7665 (mtt90)
REVERT: A   63 ARG cc_start: 0.8370 (mmp80) cc_final: 0.7838 (mmt-90)
REVERT: A   83 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.6775 (mtm180)
REVERT: A  106 ASP cc_start: 0.7627 (m-30) cc_final: 0.7398 (m-30)
REVERT: B   95 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7370 (mtp-110)
REVERT: D   62 MET cc_start: 0.8572 (mmp) cc_final: 0.8338 (mmt)
REVERT: D   71 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7113 (mp0)
REVERT: E   40 ARG cc_start: 0.8277 (mmm160) cc_final: 0.8069 (mtp180)
REVERT: E  133 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6889 (mt-10)
REVERT: G   73 ASN cc_start: 0.8133 (t0) cc_final: 0.7722 (t160)
REVERT: G   91 GLU cc_start: 0.6413 (OUTLIER) cc_final: 0.5094 (tp30)
REVERT: H   93 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7060 (mp0)
  outliers start: 10
  outliers final: 2
  residues processed: 97
  average time/residue: 1.0992
  time to fit residues: 111.6724
Evaluate side-chains
  98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain G residue   40 SER
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 9 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0980
   chunk 88 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   chunk 67 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 93 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 125 GLN
B  93 GLN
C  73 ASN
F  27 GLN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.114534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.098641 restraints weight = 15911.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 0.82
r_work: 0.3121 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  13166  Z= 0.137
  Angle     :  0.634   6.935  19112  Z= 0.374
  Chirality :  0.048   0.231   2171
  Planarity :  0.004   0.040   1347
  Dihedral  : 30.859 175.719   4223
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 20.06 %
    Favored  : 78.49 %
  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:  3.04 (0.30), residues: 737
  helix:  2.77 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.30 (0.38), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  52 
 TYR   0.014   0.002   TYR F  88 
 PHE   0.007   0.001   PHE A  67 
 HIS   0.004   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00205 /  0.14 (13166)
  covalent geometry    : angle       0.63382 /  0.37 (19112)
  hydrogen bonds       : bond        0.05188 /  3.48 (  810)
  hydrogen bonds       : angle       2.78741 /  2.10 ( 2008)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4224.59 seconds
wall clock time: 72 minutes 37.17 seconds (4357.17 seconds total)