Starting phenix.real_space_refine
on Wed Jul 30 05:39:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jl9_36389/07_2025/8jl9_36389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jl9_36389/07_2025/8jl9_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jl9_36389/07_2025/8jl9_36389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jl9_36389/07_2025/8jl9_36389.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jl9_36389/07_2025/8jl9_36389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jl9_36389/07_2025/8jl9_36389.cif"
  }
  resolution = 2.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.43, per 1000 atoms: 0.60
  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: 2.78
  Conformation dependent library (CDL) restraints added in 874.4 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: 5.94
  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: 4.93

  Time building geometry restraints manager: 3.42 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=" CZ  ARG E 131 "
       pdb=" NH2 ARG E 131 "
    ideal  model  delta    sigma   weight residual
    1.330  1.285  0.045 1.30e-02 5.92e+03 1.22e+01
  bond pdb=" CZ  ARG G  88 "
       pdb=" NH2 ARG G  88 "
    ideal  model  delta    sigma   weight residual
    1.330  1.288  0.042 1.30e-02 5.92e+03 1.02e+01
  bond pdb=" CZ  ARG E 116 "
       pdb=" NH2 ARG E 116 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.45e+00
  bond pdb=" CZ  ARG D  72 "
       pdb=" NH2 ARG D  72 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.27e+00
  ... (remaining 13161 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 18407
        2.25 -     4.50: 671
        4.50 -     6.75: 33
        6.75 -     9.00: 0
        9.00 -    11.25: 1
  Bond angle restraints: 19112
  Sorted by residual:
  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=" O   SER D  32 "
        pdb=" C   SER D  32 "
        pdb=" N   ARG D  33 "
      ideal   model   delta    sigma   weight residual
     122.59  116.13    6.46 1.33e+00 5.65e-01 2.36e+01
  angle pdb=" CA  PRO A  38 "
        pdb=" N   PRO A  38 "
        pdb=" CD  PRO A  38 "
      ideal   model   delta    sigma   weight residual
     112.00  106.41    5.59 1.40e+00 5.10e-01 1.60e+01
  angle pdb=" CA  ILE H  61 "
        pdb=" CB  ILE H  61 "
        pdb=" CG1 ILE H  61 "
      ideal   model   delta    sigma   weight residual
     110.40  117.02   -6.62 1.70e+00 3.46e-01 1.52e+01
  angle pdb=" CD  ARG E 131 "
        pdb=" NE  ARG E 131 "
        pdb=" CZ  ARG E 131 "
      ideal   model   delta    sigma   weight residual
     124.40  129.82   -5.42 1.40e+00 5.10e-01 1.50e+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: 2123
       0.119 -    0.238: 41
       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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.790
  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:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     33.930
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.050
  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:13.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6287
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.111  13166  Z= 0.308
  Angle     :  0.857  11.254  19112  Z= 0.565
  Chirality :  0.048   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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 HIS   0.006   0.001   HIS H 109 
 PHE   0.012   0.002   PHE A  84 
 TYR   0.099   0.004   TYR D  40 
 ARG   0.005   0.001   ARG A  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10462 (  810)
  hydrogen bonds       : angle       4.26159 ( 2008)
  covalent geometry    : bond        0.00548 (13166)
  covalent geometry    : angle       0.85675 (19112)

*********************** 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  : 0.843 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.7253 (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: 2.0072
  time to fit residues: 308.8601
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  : 0.940 
-------------------------------------------------------------------------------
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 84 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
A  68 GLN
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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.116387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.100724 restraints weight = 16052.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 0.81
r_work: 0.3157 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 2.80 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13166  Z= 0.194
  Angle     :  0.571   5.029  19112  Z= 0.355
  Chirality :  0.036   0.134   2171
  Planarity :  0.004   0.036   1347
  Dihedral  : 30.304 170.437   4225
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 17.66 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.82 (0.30), residues: 737
  helix:  2.60 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.30 (0.38), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 113 
 PHE   0.006   0.001   PHE E  67 
 TYR   0.012   0.001   TYR H  40 
 ARG   0.005   0.000   ARG C  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04687 (  810)
  hydrogen bonds       : angle       2.83295 ( 2008)
  covalent geometry    : bond        0.00429 (13166)
  covalent geometry    : angle       0.57140 (19112)

*********************** 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
  128 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.938 
Fit side-chains
REVERT: A   40 ARG cc_start: 0.8293 (mtp-110) cc_final: 0.7953 (mtt-85)
REVERT: A   83 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.6468 (mtm180)
REVERT: A  106 ASP cc_start: 0.7586 (m-30) cc_final: 0.7375 (m-30)
REVERT: A  128 ARG cc_start: 0.8697 (mtp180) cc_final: 0.8431 (mmm160)
REVERT: C  104 GLN cc_start: 0.7910 (tp40) cc_final: 0.7595 (mp10)
REVERT: D   71 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7362 (mt-10)
REVERT: E  120 MET cc_start: 0.7923 (mtt) cc_final: 0.7721 (mtm)
REVERT: G   73 ASN cc_start: 0.7937 (t0) cc_final: 0.7649 (t160)
REVERT: G   89 ASN cc_start: 0.8648 (m-40) cc_final: 0.8393 (m110)
REVERT: H   85 LYS cc_start: 0.8537 (mttp) cc_final: 0.8290 (mttp)
  outliers start: 9
  outliers final: 1
  residues processed: 120
  average time/residue: 2.0197
  time to fit residues: 255.1160
Evaluate side-chains
  109 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 106
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain H residue   87 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 26 optimal weight:    0.3980
   chunk 64 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
C  73 ASN
F  25 ASN
** G  84 GLN ** 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 = 0.3492 r_free = 0.3492 target = 0.116801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.101189 restraints weight = 16054.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 0.81
r_work: 0.3145 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13166  Z= 0.186
  Angle     :  0.551   5.221  19112  Z= 0.342
  Chirality :  0.035   0.121   2171
  Planarity :  0.004   0.041   1347
  Dihedral  : 30.210 172.879   4223
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 19.26 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.15 (0.30), residues: 737
  helix:  2.84 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.20 (0.38), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 113 
 PHE   0.006   0.001   PHE A  67 
 TYR   0.010   0.001   TYR D  40 
 ARG   0.005   0.000   ARG C  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04435 (  810)
  hydrogen bonds       : angle       2.71445 ( 2008)
  covalent geometry    : bond        0.00409 (13166)
  covalent geometry    : angle       0.55140 (19112)

*********************** 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
  120 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.910 
Fit side-chains
REVERT: A   83 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.6508 (mtm180)
REVERT: A  106 ASP cc_start: 0.7576 (m-30) cc_final: 0.7370 (m-30)
REVERT: A  128 ARG cc_start: 0.8660 (mtp180) cc_final: 0.8294 (mmm160)
REVERT: C  104 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7635 (mp10)
REVERT: D   71 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7127 (mp0)
REVERT: E  120 MET cc_start: 0.7973 (mtt) cc_final: 0.7762 (mtm)
REVERT: G   20 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8202 (mtm-85)
REVERT: G   73 ASN cc_start: 0.8104 (t0) cc_final: 0.7724 (t0)
REVERT: G   91 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.5004 (tp30)
  outliers start: 11
  outliers final: 2
  residues processed: 113
  average time/residue: 2.1682
  time to fit residues: 257.1992
Evaluate side-chains
  110 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain G residue   20 ARG
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   87 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0770
   chunk 40 optimal weight:    0.5980
   chunk 67 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.8540

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
F  25 ASN
F  27 GLN
** 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 = 0.3479 r_free = 0.3479 target = 0.116005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.101015 restraints weight = 16396.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 0.78
r_work: 0.3158 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13166  Z= 0.186
  Angle     :  0.548   5.033  19112  Z= 0.341
  Chirality :  0.035   0.125   2171
  Planarity :  0.004   0.043   1347
  Dihedral  : 30.105 175.029   4223
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 17.34 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.18 (0.30), residues: 737
  helix:  2.85 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.09 (0.39), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 113 
 PHE   0.008   0.001   PHE D  70 
 TYR   0.010   0.001   TYR D  40 
 ARG   0.005   0.000   ARG C  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04366 (  810)
  hydrogen bonds       : angle       2.65647 ( 2008)
  covalent geometry    : bond        0.00409 (13166)
  covalent geometry    : angle       0.54799 (19112)

*********************** 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
  116 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.891 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7802 (mtt90) cc_final: 0.7503 (mtt90)
REVERT: A   83 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.6773 (mtm180)
REVERT: A  128 ARG cc_start: 0.8649 (mtp180) cc_final: 0.8274 (mmm160)
REVERT: B   95 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7447 (mtt-85)
REVERT: C   73 ASN cc_start: 0.8076 (t160) cc_final: 0.7816 (t0)
REVERT: C   91 GLU cc_start: 0.5634 (OUTLIER) cc_final: 0.5332 (tp30)
REVERT: C  104 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7600 (mp10)
REVERT: D   71 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7178 (mp0)
REVERT: E  120 MET cc_start: 0.7969 (mtt) cc_final: 0.7767 (mtm)
REVERT: G   20 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8173 (mtm-85)
REVERT: G   73 ASN cc_start: 0.8190 (t0) cc_final: 0.7855 (t0)
REVERT: G   91 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.4913 (tp30)
REVERT: H   59 MET cc_start: 0.8691 (tpt) cc_final: 0.8208 (tpt)
REVERT: H   79 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7795 (mtt90)
  outliers start: 19
  outliers final: 4
  residues processed: 108
  average time/residue: 2.2496
  time to fit residues: 254.9377
Evaluate side-chains
  105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
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   91 GLU
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain G residue   20 ARG
Chi-restraints excluded: chain G residue   40 SER
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   79 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 94 optimal weight:    1.9990
   chunk 70 optimal weight:    7.9990
   chunk 99 optimal weight:    3.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
D  84 ASN
E  68 GLN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.110131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.094792 restraints weight = 16287.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 0.81
r_work: 0.3068 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.2854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042  13166  Z= 0.314
  Angle     :  0.636   6.449  19112  Z= 0.386
  Chirality :  0.043   0.145   2171
  Planarity :  0.005   0.047   1347
  Dihedral  : 30.214 176.085   4223
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.78 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.65 (0.30), residues: 737
  helix:  2.47 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.33 (0.38), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS A 113 
 PHE   0.008   0.002   PHE H  70 
 TYR   0.019   0.002   TYR D  40 
 ARG   0.011   0.001   ARG E  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05889 (  810)
  hydrogen bonds       : angle       2.87118 ( 2008)
  covalent geometry    : bond        0.00722 (13166)
  covalent geometry    : angle       0.63642 (19112)

*********************** 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
  107 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 1.327 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7917 (mtt90) cc_final: 0.7673 (mtt90)
REVERT: A   83 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.6845 (mtm180)
REVERT: B   95 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7364 (mtp-110)
REVERT: C   91 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.4300 (tp30)
REVERT: C  104 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7541 (mp10)
REVERT: D   71 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7247 (mp0)
REVERT: G   73 ASN cc_start: 0.8254 (t0) cc_final: 0.7845 (t0)
REVERT: G   91 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.4914 (tp30)
  outliers start: 16
  outliers final: 7
  residues processed: 100
  average time/residue: 2.8403
  time to fit residues: 297.6231
Evaluate side-chains
  105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain G residue   40 SER
Chi-restraints excluded: chain G residue   91 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0570
   chunk 70 optimal weight:    7.9990
   chunk 65 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.112487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.097240 restraints weight = 16367.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 0.79
r_work: 0.3106 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13166  Z= 0.169
  Angle     :  0.588   5.871  19112  Z= 0.364
  Chirality :  0.037   0.127   2171
  Planarity :  0.004   0.047   1347
  Dihedral  : 30.265 175.539   4223
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 19.26 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.88 (0.30), residues: 737
  helix:  2.65 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.28 (0.39), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 113 
 PHE   0.009   0.001   PHE D  70 
 TYR   0.026   0.001   TYR F  88 
 ARG   0.003   0.000   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04811 (  810)
  hydrogen bonds       : angle       2.81913 ( 2008)
  covalent geometry    : bond        0.00362 (13166)
  covalent geometry    : angle       0.58807 (19112)

*********************** 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
  101 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.843 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7851 (mtt90) cc_final: 0.7579 (mtt90)
REVERT: B   95 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7564 (mtp-110)
REVERT: C   91 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.4858 (tp30)
REVERT: C  104 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7513 (mp10)
REVERT: D   71 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7113 (mp0)
REVERT: E  133 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6986 (mt-10)
REVERT: G   73 ASN cc_start: 0.8205 (t0) cc_final: 0.7915 (t160)
REVERT: G   91 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.4823 (tp30)
REVERT: H   59 MET cc_start: 0.8729 (tpt) cc_final: 0.8053 (tpt)
  outliers start: 13
  outliers final: 3
  residues processed: 93
  average time/residue: 2.4811
  time to fit residues: 241.4549
Evaluate side-chains
  98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue   87 SER
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain G residue   91 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
B  93 GLN
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.113502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.098554 restraints weight = 16460.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 0.77
r_work: 0.3119 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  13166  Z= 0.215
  Angle     :  0.570   8.009  19112  Z= 0.351
  Chirality :  0.037   0.127   2171
  Planarity :  0.004   0.046   1347
  Dihedral  : 30.213 174.458   4223
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 18.94 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.95 (0.30), residues: 737
  helix:  2.70 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.26 (0.39), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 113 
 PHE   0.005   0.001   PHE C  25 
 TYR   0.010   0.001   TYR D  40 
 ARG   0.006   0.000   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04622 (  810)
  hydrogen bonds       : angle       2.70349 ( 2008)
  covalent geometry    : bond        0.00481 (13166)
  covalent geometry    : angle       0.57003 (19112)

*********************** 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
  106 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 1.305 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7832 (mtt90) cc_final: 0.7589 (mtt90)
REVERT: B   95 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7394 (mtp-110)
REVERT: C   91 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.4649 (tp30)
REVERT: C  104 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7499 (mp10)
REVERT: D   71 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7160 (mp0)
REVERT: E   40 ARG cc_start: 0.8273 (mtp180) cc_final: 0.8050 (mtp180)
REVERT: E  133 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7029 (mt-10)
REVERT: G   73 ASN cc_start: 0.8224 (t0) cc_final: 0.7828 (t0)
REVERT: G   91 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.4926 (tp30)
  outliers start: 13
  outliers final: 4
  residues processed: 99
  average time/residue: 2.5889
  time to fit residues: 268.2704
Evaluate side-chains
  105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain G residue   20 ARG
Chi-restraints excluded: chain G residue   91 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
B  93 GLN
C  73 ASN
F  25 ASN
F  75 HIS
** 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 = 0.3399 r_free = 0.3399 target = 0.110398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.095102 restraints weight = 16409.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 0.80
r_work: 0.3071 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041  13166  Z= 0.292
  Angle     :  0.622   8.241  19112  Z= 0.378
  Chirality :  0.042   0.143   2171
  Planarity :  0.005   0.048   1347
  Dihedral  : 30.237 174.944   4223
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 19.42 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.63 (0.30), residues: 737
  helix:  2.45 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.33 (0.39), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS A 113 
 PHE   0.008   0.002   PHE H  70 
 TYR   0.018   0.002   TYR D  40 
 ARG   0.005   0.001   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05594 (  810)
  hydrogen bonds       : angle       2.83482 ( 2008)
  covalent geometry    : bond        0.00668 (13166)
  covalent geometry    : angle       0.62169 (19112)

*********************** 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: 13
    poor density    : 89
  time to evaluate  : 0.949 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7882 (mtt90) cc_final: 0.7637 (mtt90)
REVERT: B   95 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7385 (mtp-110)
REVERT: C   91 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.4188 (tp30)
REVERT: C  104 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7494 (mp10)
REVERT: D   71 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7188 (mp0)
REVERT: E  133 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7048 (mt-10)
REVERT: G   73 ASN cc_start: 0.8261 (t0) cc_final: 0.7865 (t0)
REVERT: G   91 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.5851 (tp30)
  outliers start: 13
  outliers final: 4
  residues processed: 97
  average time/residue: 2.2068
  time to fit residues: 224.8471
Evaluate side-chains
  99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain G residue   91 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 83 optimal weight:    3.9990
   chunk 2 optimal weight:    0.1980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
B  25 ASN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
F  25 ASN
** 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 = 0.3425 r_free = 0.3425 target = 0.112229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.096976 restraints weight = 16303.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 0.79
r_work: 0.3102 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13166  Z= 0.174
  Angle     :  0.596  10.124  19112  Z= 0.366
  Chirality :  0.036   0.129   2171
  Planarity :  0.004   0.046   1347
  Dihedral  : 30.291 174.769   4223
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 20.22 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.89 (0.31), residues: 737
  helix:  2.64 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.23 (0.39), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.006   0.001   PHE A  67 
 TYR   0.015   0.002   TYR B  88 
 ARG   0.006   0.000   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04770 (  810)
  hydrogen bonds       : angle       2.80485 ( 2008)
  covalent geometry    : bond        0.00374 (13166)
  covalent geometry    : angle       0.59623 (19112)

*********************** 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
  99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7836 (mtt90) cc_final: 0.7593 (mtt90)
REVERT: B   95 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7525 (mtp-110)
REVERT: C   91 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.4645 (tp30)
REVERT: C  104 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7479 (mp10)
REVERT: D   71 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7106 (mp0)
REVERT: E  133 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7046 (mt-10)
REVERT: G   73 ASN cc_start: 0.8229 (t0) cc_final: 0.7932 (t160)
REVERT: G   91 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.5716 (tp30)
  outliers start: 11
  outliers final: 4
  residues processed: 95
  average time/residue: 2.5202
  time to fit residues: 251.2370
Evaluate side-chains
  97 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain G residue   91 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 66 optimal weight:    0.1980
   chunk 18 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0060
   chunk 16 optimal weight:    0.0870
   overall best weight:    0.5776

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  63 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.112722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.097485 restraints weight = 16275.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 0.78
r_work: 0.3112 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13166  Z= 0.186
  Angle     :  0.583   9.670  19112  Z= 0.358
  Chirality :  0.036   0.125   2171
  Planarity :  0.004   0.046   1347
  Dihedral  : 30.264 175.137   4223
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.95 (0.30), residues: 737
  helix:  2.67 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.16 (0.40), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 113 
 PHE   0.005   0.001   PHE A  67 
 TYR   0.013   0.002   TYR F  88 
 ARG   0.008   0.000   ARG G  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04693 (  810)
  hydrogen bonds       : angle       2.74686 ( 2008)
  covalent geometry    : bond        0.00407 (13166)
  covalent geometry    : angle       0.58306 (19112)

********************** 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
  99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 1.134 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7819 (mtt90) cc_final: 0.7574 (mtt90)
REVERT: A  128 ARG cc_start: 0.8625 (mtp180) cc_final: 0.8260 (mmm160)
REVERT: B   95 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7355 (mtp-110)
REVERT: C   91 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.4552 (tp30)
REVERT: C  104 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7499 (mp10)
REVERT: D   71 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7163 (mp0)
REVERT: E  133 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7055 (mt-10)
REVERT: G   73 ASN cc_start: 0.8230 (t0) cc_final: 0.7940 (t160)
REVERT: G   91 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.5729 (tp30)
  outliers start: 11
  outliers final: 4
  residues processed: 95
  average time/residue: 2.6897
  time to fit residues: 268.4040
Evaluate side-chains
  98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain G residue   91 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
B  93 GLN
E  68 GLN
F  25 ASN
** 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 = 0.3455 r_free = 0.3455 target = 0.114198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.099018 restraints weight = 16307.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 0.78
r_work: 0.3137 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13166  Z= 0.194
  Angle     :  0.561   9.569  19112  Z= 0.346
  Chirality :  0.036   0.123   2171
  Planarity :  0.004   0.047   1347
  Dihedral  : 30.221 174.608   4223
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 20.71 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.99 (0.31), residues: 737
  helix:  2.69 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.12 (0.41), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 109 
 PHE   0.005   0.001   PHE F  61 
 TYR   0.021   0.002   TYR B  88 
 ARG   0.005   0.000   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04397 (  810)
  hydrogen bonds       : angle       2.66571 ( 2008)
  covalent geometry    : bond        0.00428 (13166)
  covalent geometry    : angle       0.56089 (19112)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8455.32 seconds
wall clock time: 151 minutes 38.99 seconds (9098.99 seconds total)