Starting phenix.real_space_refine
on Wed Sep 17 21:27:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k40_62036/09_2025/9k40_62036.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k40_62036/09_2025/9k40_62036.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k40_62036/09_2025/9k40_62036.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k40_62036/09_2025/9k40_62036.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k40_62036/09_2025/9k40_62036.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k40_62036/09_2025/9k40_62036.cif"
  }
  resolution = 3.15
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.040
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     289      5.49       5
     S      12      5.16       5
     C    6575      2.51       5
     N    2168      2.21       5
     O    2780      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11824
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 783
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 644
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 783
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 783
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 644
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 783
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "H"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2950
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2992
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 3.06, per 1000 atoms: 0.26
  Number of scatterers: 11824
  At special positions: 0
  Unit cell: (104.5, 119.9, 115.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     P     289     15.00
     O    2780      8.00
     N    2168      7.00
     C    6575      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Conformation dependent library (CDL) restraints added in 437.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1396

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 10 sheets defined
      74.1% alpha, 2.7% beta
      144 base pairs and 251 stacking pairs defined.
    Time for finding SS restraints: 1.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.632A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   SER A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.890A  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 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.503A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.536A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 27 through 38
    Processing helix  chain 'C' and resid 47 through 74
    Processing helix  chain 'C' and resid 80 through 91
    Processing helix  chain 'C' and resid 91 through 98
    Processing helix  chain 'C' and resid 113 through 117
    Processing helix  chain 'D' and resid 60 through 72
    Processing helix  chain 'D' and resid 78 through 107
    Processing helix  chain 'D' and resid 113 through 125
    Processing helix  chain 'D' and resid 126 through 147
      removed outlier: 3.715A  pdb=" N   SER D 147 " --> pdb=" O   LYS D 143 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.570A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   SER E  57 " --> pdb=" O   LYS E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.832A  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 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.552A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.541A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 22
    Processing helix  chain 'G' and resid 27 through 38
    Processing helix  chain 'G' and resid 47 through 75
    Processing helix  chain 'G' and resid 80 through 91
    Processing helix  chain 'G' and resid 91 through 98
    Processing helix  chain 'G' and resid 113 through 117
    Processing helix  chain 'H' and resid 60 through 72
    Processing helix  chain 'H' and resid 78 through 107
    Processing helix  chain 'H' and resid 113 through 125
    Processing helix  chain 'H' and resid 126 through 147
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.035A  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 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44
      removed outlier: 6.851A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103
      removed outlier: 7.092A  pdb=" N   THR C 102 " --> 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: 7.035A  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 43 through 44
      removed outlier: 6.985A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79

    408 hydrogen bonds defined for protein.
    1203 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      346 hydrogen bonds
      692 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      251 stacking parallelities
  Total time for adding SS restraints: 2.37

  Time building geometry restraints manager: 1.41 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2039
        1.33 -     1.45: 4192
        1.45 -     1.57: 5799
        1.57 -     1.69: 577
        1.69 -     1.80: 22
  Bond restraints: 12629
  Sorted by residual:
  bond pdb=" O3'  DG I -26 "
       pdb=" P    DT I -25 "
    ideal  model  delta    sigma   weight residual
    1.607  1.657 -0.050 1.50e-02 4.44e+03 1.11e+01
  bond pdb=" O3'  DA J -46 "
       pdb=" P    DA J -45 "
    ideal  model  delta    sigma   weight residual
    1.607  1.655 -0.048 1.50e-02 4.44e+03 1.04e+01
  bond pdb=" O3'  DC J -24 "
       pdb=" P    DC J -23 "
    ideal  model  delta    sigma   weight residual
    1.607  1.654 -0.047 1.50e-02 4.44e+03 1.00e+01
  bond pdb=" O3'  DT J -36 "
       pdb=" P    DG J -35 "
    ideal  model  delta    sigma   weight residual
    1.607  1.654 -0.047 1.50e-02 4.44e+03 1.00e+01
  bond pdb=" O3'  DA J -49 "
       pdb=" P    DG J -48 "
    ideal  model  delta    sigma   weight residual
    1.607  1.644 -0.037 1.50e-02 4.44e+03 6.14e+00
  ... (remaining 12624 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 17597
        1.43 -     2.86: 639
        2.86 -     4.28: 48
        4.28 -     5.71: 15
        5.71 -     7.14: 4
  Bond angle restraints: 18303
  Sorted by residual:
  angle pdb=" N   ASN F  25 "
        pdb=" CA  ASN F  25 "
        pdb=" C   ASN F  25 "
      ideal   model   delta    sigma   weight residual
     112.92  106.83    6.09 1.23e+00 6.61e-01 2.45e+01
  angle pdb=" O3'  DG J -37 "
        pdb=" C3'  DG J -37 "
        pdb=" C2'  DG J -37 "
      ideal   model   delta    sigma   weight residual
     111.50  105.24    6.26 1.50e+00 4.44e-01 1.74e+01
  angle pdb=" N   GLY D 127 "
        pdb=" CA  GLY D 127 "
        pdb=" C   GLY D 127 "
      ideal   model   delta    sigma   weight residual
     111.02  118.16   -7.14 1.86e+00 2.89e-01 1.47e+01
  angle pdb=" N   GLY H 127 "
        pdb=" CA  GLY H 127 "
        pdb=" C   GLY H 127 "
      ideal   model   delta    sigma   weight residual
     111.34  118.26   -6.92 1.82e+00 3.02e-01 1.45e+01
  angle pdb=" N   ILE F  26 "
        pdb=" CA  ILE F  26 "
        pdb=" C   ILE F  26 "
      ideal   model   delta    sigma   weight residual
     111.09  106.72    4.37 1.25e+00 6.40e-01 1.22e+01
  ... (remaining 18298 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.21: 4295
       18.21 -    36.42: 1209
       36.42 -    54.64: 1118
       54.64 -    72.85: 287
       72.85 -    91.06: 22
  Dihedral angle restraints: 6931
    sinusoidal: 4773
      harmonic: 2158
  Sorted by residual:
  dihedral pdb=" CA  ASN G  69 "
           pdb=" CB  ASN G  69 "
           pdb=" CG  ASN G  69 "
           pdb=" OD1 ASN G  69 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -173.40  -66.60     2      2.00e+01 2.50e-03 1.01e+01
  dihedral pdb=" CA  PRO H 126 "
           pdb=" C   PRO H 126 "
           pdb=" N   GLY H 127 "
           pdb=" CA  GLY H 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.14   15.86     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CA  PRO D 126 "
           pdb=" C   PRO D 126 "
           pdb=" N   GLY D 127 "
           pdb=" CA  GLY D 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.51   15.49     0      5.00e+00 4.00e-02 9.60e+00
  ... (remaining 6928 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1723
       0.044 -    0.088: 300
       0.088 -    0.132: 55
       0.132 -    0.176: 10
       0.176 -    0.220: 1
  Chirality restraints: 2089
  Sorted by residual:
  chirality pdb=" C3'  DG J -37 "
            pdb=" C4'  DG J -37 "
            pdb=" O3'  DG J -37 "
            pdb=" C2'  DG J -37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.88    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" C3'  DC J -26 "
            pdb=" C4'  DC J -26 "
            pdb=" O3'  DC J -26 "
            pdb=" C2'  DC J -26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.83    0.17 2.00e-01 2.50e+01 7.36e-01
  chirality pdb=" C3'  DG J -47 "
            pdb=" C4'  DG J -47 "
            pdb=" O3'  DG J -47 "
            pdb=" C2'  DG J -47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.82    0.16 2.00e-01 2.50e+01 6.67e-01
  ... (remaining 2086 not shown)

  Planarity restraints: 1310
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN G  74 "    0.011 2.00e-02 2.50e+03   2.18e-02 4.74e+00
        pdb=" C   ASN G  74 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   ASN G  74 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LYS G  75 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 125 "   -0.028 5.00e-02 4.00e+02   4.23e-02 2.86e+00
        pdb=" N   PRO D 126 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO D 126 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO D 126 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H 125 "    0.027 5.00e-02 4.00e+02   4.15e-02 2.76e+00
        pdb=" N   PRO H 126 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO H 126 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO H 126 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1307 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1553
        2.75 -     3.29: 10323
        3.29 -     3.83: 23082
        3.83 -     4.36: 27355
        4.36 -     4.90: 39301
  Nonbonded interactions: 101614
  Sorted by model distance:
  nonbonded pdb=" OG  SER G  19 "
            pdb=" O   PHE G  26 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" NH2 ARG C  33 "
            pdb=" OE1 GLU D  58 "
     model   vdw
     2.282 3.120
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH1 ARG A 131 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH1 ARG E 131 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" OG1 THR F  73 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.334 3.040
  ... (remaining 101609 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'
  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'
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.790
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.920
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12629  Z= 0.189
  Angle     :  0.606   7.139  18303  Z= 0.375
  Chirality :  0.036   0.220   2089
  Planarity :  0.004   0.042   1310
  Dihedral  : 28.829  91.058   5535
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 11.33 %
    Favored  : 88.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.72 (0.30), residues: 730
  helix:  2.37 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop :  0.25 (0.39), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  72 
 TYR   0.019   0.001   TYR F  98 
 PHE   0.008   0.001   PHE H  88 
 HIS   0.002   0.001   HIS D  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (12629)
  covalent geometry    : angle       0.60648 (18303)
  hydrogen bonds       : bond        0.11525 (  754)
  hydrogen bonds       : angle       3.89656 ( 1895)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 228
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 0
  residues processed: 230
  average time/residue: 0.1291
  time to fit residues: 40.5179
Evaluate side-chains
  196 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0050
   chunk 61 optimal weight:    0.1980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
B  75 HIS
B  93 GLN
C  83 HIS
D  86 ASN
D 107 ASN
E  68 GLN
G  69 ASN
G  74 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.070318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.049718 restraints weight = 49726.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 2.24
r_work: 0.2812 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
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   0.026  12629  Z= 0.148
  Angle     :  0.575   6.016  18303  Z= 0.349
  Chirality :  0.035   0.136   2089
  Planarity :  0.004   0.035   1310
  Dihedral  : 31.334  89.128   4071
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 16.99 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.21 (0.30), residues: 730
  helix:  2.75 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop :  0.24 (0.41), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 122 
 TYR   0.014   0.002   TYR D  63 
 PHE   0.008   0.001   PHE A  67 
 HIS   0.005   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (12629)
  covalent geometry    : angle       0.57510 (18303)
  hydrogen bonds       : bond        0.03876 (  754)
  hydrogen bonds       : angle       2.85263 ( 1895)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 216
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8405 (pt0) cc_final: 0.8185 (pm20)
REVERT: A   81 ASP cc_start: 0.8523 (t0) cc_final: 0.8278 (t0)
REVERT: B   84 MET cc_start: 0.8994 (mmm) cc_final: 0.8590 (mmm)
REVERT: C   65 GLU cc_start: 0.8682 (tp30) cc_final: 0.8462 (tp30)
REVERT: C   92 GLU cc_start: 0.9021 (tp30) cc_final: 0.8773 (tp30)
REVERT: D   91 ASP cc_start: 0.9346 (t0) cc_final: 0.9110 (t0)
REVERT: E   59 GLU cc_start: 0.8301 (pt0) cc_final: 0.8088 (pm20)
REVERT: F   84 MET cc_start: 0.8925 (mmm) cc_final: 0.8099 (mmm)
REVERT: G   91 ASP cc_start: 0.8174 (t0) cc_final: 0.7849 (t70)
REVERT: H   94 GLU cc_start: 0.9018 (tp30) cc_final: 0.8618 (tp30)
REVERT: H   98 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8350 (mm-40)
REVERT: H  128 GLU cc_start: 0.8311 (tp30) cc_final: 0.7756 (tp30)
  outliers start: 9
  outliers final: 4
  residues processed: 222
  average time/residue: 0.1220
  time to fit residues: 37.1615
Evaluate side-chains
  203 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 199
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   97 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 9 optimal weight:    0.2980
   chunk 92 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 88 optimal weight:    8.9990
   chunk 95 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 17 optimal weight:   10.0000
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
D  86 ASN
E  68 GLN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  74 ASN
H 132 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.069965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.049245 restraints weight = 50170.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 2.25
r_work: 0.2809 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.2290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  12629  Z= 0.147
  Angle     :  0.556   6.591  18303  Z= 0.338
  Chirality :  0.033   0.140   2089
  Planarity :  0.004   0.041   1310
  Dihedral  : 31.401  87.512   4071
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 17.80 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.51 (0.30), residues: 730
  helix:  3.02 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop :  0.12 (0.41), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 122 
 TYR   0.020   0.002   TYR D 106 
 PHE   0.006   0.001   PHE A  41 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (12629)
  covalent geometry    : angle       0.55596 (18303)
  hydrogen bonds       : bond        0.03722 (  754)
  hydrogen bonds       : angle       2.74936 ( 1895)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 203
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8615 (t0) cc_final: 0.8341 (t0)
REVERT: B   84 MET cc_start: 0.9020 (mmm) cc_final: 0.8526 (mmm)
REVERT: B   88 TYR cc_start: 0.9369 (m-10) cc_final: 0.8775 (m-10)
REVERT: C   65 GLU cc_start: 0.8715 (tp30) cc_final: 0.8394 (tp30)
REVERT: D   91 ASP cc_start: 0.9336 (t0) cc_final: 0.9101 (t0)
REVERT: D   94 GLU cc_start: 0.9087 (tp30) cc_final: 0.8584 (tp30)
REVERT: D   98 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8504 (mm-40)
REVERT: E   81 ASP cc_start: 0.8793 (m-30) cc_final: 0.8436 (t0)
REVERT: G   75 LYS cc_start: 0.9376 (mtmm) cc_final: 0.9102 (mtmm)
REVERT: G   91 ASP cc_start: 0.8137 (t0) cc_final: 0.7729 (t70)
REVERT: G   92 GLU cc_start: 0.8934 (tp30) cc_final: 0.8702 (tp30)
REVERT: G   93 GLU cc_start: 0.9297 (mp0) cc_final: 0.8927 (mp0)
REVERT: H  128 GLU cc_start: 0.7996 (tp30) cc_final: 0.7795 (tp30)
  outliers start: 8
  outliers final: 6
  residues processed: 206
  average time/residue: 0.1207
  time to fit residues: 34.0723
Evaluate side-chains
  197 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 191
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   86 ASN
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain F residue   97 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 94 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 86 optimal weight:   10.0000
   chunk 82 optimal weight:    6.9990
   chunk 67 optimal weight:    0.8980
   chunk 95 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 85 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
D  86 ASN
E 113 HIS
F  75 HIS
G 114 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.065831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.045141 restraints weight = 50921.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 2.26
r_work: 0.2686 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8776
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  12629  Z= 0.219
  Angle     :  0.597   9.217  18303  Z= 0.360
  Chirality :  0.036   0.149   2089
  Planarity :  0.004   0.037   1310
  Dihedral  : 31.899  89.813   4071
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 17.96 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.46 (0.30), residues: 730
  helix:  2.99 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop :  0.06 (0.41), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 105 
 TYR   0.017   0.002   TYR H 106 
 PHE   0.008   0.001   PHE C  26 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 (12629)
  covalent geometry    : angle       0.59749 (18303)
  hydrogen bonds       : bond        0.05224 (  754)
  hydrogen bonds       : angle       3.00755 ( 1895)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 200
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.9415 (tttm) cc_final: 0.9103 (tttm)
REVERT: A   59 GLU cc_start: 0.8915 (pm20) cc_final: 0.8575 (pm20)
REVERT: A   73 GLU cc_start: 0.8848 (tp30) cc_final: 0.7817 (tp30)
REVERT: A   81 ASP cc_start: 0.8834 (t0) cc_final: 0.8535 (t0)
REVERT: C   65 GLU cc_start: 0.8805 (tp30) cc_final: 0.8437 (tp30)
REVERT: C  102 THR cc_start: 0.9437 (m) cc_final: 0.9134 (t)
REVERT: C  111 ASN cc_start: 0.9008 (p0) cc_final: 0.8681 (p0)
REVERT: D  143 LYS cc_start: 0.9665 (OUTLIER) cc_final: 0.9278 (tttp)
REVERT: E   53 LYS cc_start: 0.9399 (tttm) cc_final: 0.9069 (tttm)
REVERT: E   59 GLU cc_start: 0.8871 (pm20) cc_final: 0.8595 (pm20)
REVERT: E   81 ASP cc_start: 0.8893 (m-30) cc_final: 0.8573 (t0)
REVERT: F   84 MET cc_start: 0.9136 (mmm) cc_final: 0.8485 (mmm)
REVERT: G   21 LYS cc_start: 0.9453 (mmmt) cc_final: 0.9069 (tptm)
REVERT: G   65 GLU cc_start: 0.8823 (tp30) cc_final: 0.8587 (tp30)
REVERT: G   91 ASP cc_start: 0.8343 (t0) cc_final: 0.8006 (t70)
REVERT: G   92 GLU cc_start: 0.9063 (tp30) cc_final: 0.8852 (tp30)
  outliers start: 13
  outliers final: 6
  residues processed: 204
  average time/residue: 0.1203
  time to fit residues: 33.5494
Evaluate side-chains
  194 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 187
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue  114 ASN
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue  143 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain F residue   97 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 91 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 94 optimal weight:    4.9990
   chunk 90 optimal weight:    5.9990
   chunk 35 optimal weight:    0.8980
   chunk 62 optimal weight:   10.0000
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
D  86 ASN
D 132 HIS
E  68 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.066316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.045772 restraints weight = 50615.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 2.28
r_work: 0.2716 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8757
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  12629  Z= 0.178
  Angle     :  0.581   7.250  18303  Z= 0.350
  Chirality :  0.034   0.158   2089
  Planarity :  0.004   0.039   1310
  Dihedral  : 31.672  89.645   4071
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.42 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.58 (0.30), residues: 730
  helix:  3.10 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop :  0.02 (0.42), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 122 
 TYR   0.025   0.002   TYR B  88 
 PHE   0.007   0.001   PHE D  88 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (12629)
  covalent geometry    : angle       0.58104 (18303)
  hydrogen bonds       : bond        0.04108 (  754)
  hydrogen bonds       : angle       2.81996 ( 1895)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 200
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.9420 (tttm) cc_final: 0.9130 (tttm)
REVERT: A   59 GLU cc_start: 0.8936 (pm20) cc_final: 0.8570 (pm20)
REVERT: A   81 ASP cc_start: 0.8859 (t0) cc_final: 0.8542 (t0)
REVERT: B   84 MET cc_start: 0.9164 (mmm) cc_final: 0.8695 (mmm)
REVERT: B   88 TYR cc_start: 0.9346 (m-10) cc_final: 0.8907 (m-10)
REVERT: C   65 GLU cc_start: 0.8768 (tp30) cc_final: 0.8379 (tp30)
REVERT: C   92 GLU cc_start: 0.9044 (tp30) cc_final: 0.8795 (tp30)
REVERT: C  111 ASN cc_start: 0.8882 (p0) cc_final: 0.8352 (p0)
REVERT: D   94 GLU cc_start: 0.9217 (tp30) cc_final: 0.8756 (tp30)
REVERT: D   98 GLN cc_start: 0.9309 (mm-40) cc_final: 0.8820 (mm-40)
REVERT: E   53 LYS cc_start: 0.9420 (tttm) cc_final: 0.9108 (tttm)
REVERT: E   59 GLU cc_start: 0.8824 (pm20) cc_final: 0.8545 (pm20)
REVERT: E   81 ASP cc_start: 0.8911 (m-30) cc_final: 0.8646 (t0)
REVERT: G   21 LYS cc_start: 0.9448 (mmmt) cc_final: 0.9039 (tptm)
REVERT: G   65 GLU cc_start: 0.8801 (tp30) cc_final: 0.8542 (tp30)
REVERT: G   91 ASP cc_start: 0.8135 (t0) cc_final: 0.7139 (t70)
REVERT: G   92 GLU cc_start: 0.9080 (tp30) cc_final: 0.8863 (tp30)
REVERT: G   93 GLU cc_start: 0.9276 (mp0) cc_final: 0.8801 (pm20)
REVERT: H   94 GLU cc_start: 0.9155 (tp30) cc_final: 0.8542 (tp30)
REVERT: H   98 GLN cc_start: 0.9412 (mm-40) cc_final: 0.8920 (mm-40)
  outliers start: 15
  outliers final: 10
  residues processed: 205
  average time/residue: 0.1184
  time to fit residues: 33.4851
Evaluate side-chains
  202 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 192
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   86 ASN
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue  121 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 66 optimal weight:    0.4980
   chunk 27 optimal weight:    0.8980
   chunk 92 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 96 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 98 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 78 optimal weight:    4.9990
   overall best weight:    3.0786

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

Flipped N/Q/H residues before XYZ refinement:
** D  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
G  25 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.063147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.042664 restraints weight = 51024.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.2810 rms_B_bonded: 2.30
r_work: 0.2624 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8835
moved from start:          0.3587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  12629  Z= 0.281
  Angle     :  0.636   6.247  18303  Z= 0.380
  Chirality :  0.038   0.167   2089
  Planarity :  0.004   0.037   1310
  Dihedral  : 32.263  89.151   4071
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 20.87 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.31 (0.30), residues: 730
  helix:  2.92 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.16 (0.42), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 122 
 TYR   0.029   0.002   TYR B  88 
 PHE   0.011   0.002   PHE H  93 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00630 (12629)
  covalent geometry    : angle       0.63550 (18303)
  hydrogen bonds       : bond        0.06152 (  754)
  hydrogen bonds       : angle       3.21103 ( 1895)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 185
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.9383 (tttm) cc_final: 0.9043 (tttm)
REVERT: A   55 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.9018 (mt0)
REVERT: A   73 GLU cc_start: 0.8900 (tp30) cc_final: 0.8652 (tp30)
REVERT: A   81 ASP cc_start: 0.8928 (t0) cc_final: 0.8631 (t0)
REVERT: B   84 MET cc_start: 0.9177 (mmm) cc_final: 0.8723 (mmm)
REVERT: B   88 TYR cc_start: 0.9317 (m-10) cc_final: 0.9082 (m-10)
REVERT: C   65 GLU cc_start: 0.8785 (tp30) cc_final: 0.8365 (tp30)
REVERT: C   92 GLU cc_start: 0.9096 (tp30) cc_final: 0.8886 (tp30)
REVERT: C  111 ASN cc_start: 0.8835 (p0) cc_final: 0.8522 (p0)
REVERT: D   82 MET cc_start: 0.9377 (tpp) cc_final: 0.9139 (tpp)
REVERT: D   94 GLU cc_start: 0.9196 (tp30) cc_final: 0.8457 (tp30)
REVERT: D   98 GLN cc_start: 0.9422 (mm-40) cc_final: 0.8701 (mm-40)
REVERT: D  128 GLU cc_start: 0.8562 (tp30) cc_final: 0.8359 (tp30)
REVERT: D  143 LYS cc_start: 0.9697 (OUTLIER) cc_final: 0.9295 (tttp)
REVERT: E   53 LYS cc_start: 0.9384 (tttm) cc_final: 0.9034 (tttm)
REVERT: E   55 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8841 (mt0)
REVERT: F   84 MET cc_start: 0.9307 (mmm) cc_final: 0.8720 (mmm)
REVERT: G   21 LYS cc_start: 0.9449 (mmmt) cc_final: 0.8898 (tptm)
REVERT: G   65 GLU cc_start: 0.8821 (tp30) cc_final: 0.8564 (tp30)
REVERT: G   91 ASP cc_start: 0.8462 (t70) cc_final: 0.7758 (t70)
REVERT: G   92 GLU cc_start: 0.9092 (tp30) cc_final: 0.8847 (tp30)
REVERT: G   93 GLU cc_start: 0.9300 (mp0) cc_final: 0.8802 (pm20)
REVERT: H   94 GLU cc_start: 0.9080 (tp30) cc_final: 0.8332 (tp30)
REVERT: H   98 GLN cc_start: 0.9422 (mm-40) cc_final: 0.8770 (mm-40)
REVERT: H  128 GLU cc_start: 0.8488 (tp30) cc_final: 0.8284 (tp30)
  outliers start: 18
  outliers final: 9
  residues processed: 191
  average time/residue: 0.1244
  time to fit residues: 32.3853
Evaluate side-chains
  192 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 180
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue  143 LYS
Chi-restraints excluded: chain E residue   55 GLN
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue   89 ILE
Chi-restraints excluded: chain H residue  121 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 88 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 86 optimal weight:   10.0000
   chunk 97 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** D  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
G  25 GLN
H  56 ASN
H  70 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.064154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.044227 restraints weight = 50883.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.2877 rms_B_bonded: 2.30
r_work: 0.2696 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8783
moved from start:          0.3701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12629  Z= 0.171
  Angle     :  0.582   6.770  18303  Z= 0.352
  Chirality :  0.035   0.164   2089
  Planarity :  0.004   0.038   1310
  Dihedral  : 31.794  89.187   4071
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 21.68 %
    Favored  : 75.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.59 (0.31), residues: 730
  helix:  3.13 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.13 (0.42), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 122 
 TYR   0.022   0.002   TYR B  88 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (12629)
  covalent geometry    : angle       0.58225 (18303)
  hydrogen bonds       : bond        0.04175 (  754)
  hydrogen bonds       : angle       2.86023 ( 1895)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 199
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.9436 (tttm) cc_final: 0.9138 (tttm)
REVERT: A   55 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8904 (mt0)
REVERT: A   73 GLU cc_start: 0.8907 (tp30) cc_final: 0.8693 (tp30)
REVERT: A   81 ASP cc_start: 0.8833 (t0) cc_final: 0.8531 (t0)
REVERT: B   84 MET cc_start: 0.9070 (mmm) cc_final: 0.8766 (mmm)
REVERT: C   65 GLU cc_start: 0.8723 (tp30) cc_final: 0.8300 (tp30)
REVERT: C  111 ASN cc_start: 0.8860 (p0) cc_final: 0.8554 (p0)
REVERT: D   82 MET cc_start: 0.9328 (tpp) cc_final: 0.9091 (tpp)
REVERT: D   94 GLU cc_start: 0.9206 (tp30) cc_final: 0.8257 (tp30)
REVERT: D   98 GLN cc_start: 0.9425 (mm-40) cc_final: 0.8495 (mm-40)
REVERT: D  143 LYS cc_start: 0.9673 (OUTLIER) cc_final: 0.9298 (tttp)
REVERT: E   53 LYS cc_start: 0.9434 (tttm) cc_final: 0.9108 (tttm)
REVERT: E   73 GLU cc_start: 0.8911 (tp30) cc_final: 0.8456 (tp30)
REVERT: F   84 MET cc_start: 0.9152 (mmm) cc_final: 0.8625 (mmm)
REVERT: F   88 TYR cc_start: 0.9455 (m-10) cc_final: 0.9047 (m-10)
REVERT: G   21 LYS cc_start: 0.9402 (mmmt) cc_final: 0.8891 (tptm)
REVERT: G   65 GLU cc_start: 0.8775 (tp30) cc_final: 0.8486 (tp30)
REVERT: G   91 ASP cc_start: 0.8229 (t70) cc_final: 0.7229 (t70)
REVERT: G   93 GLU cc_start: 0.9260 (mp0) cc_final: 0.8776 (pm20)
REVERT: H   94 GLU cc_start: 0.9002 (tp30) cc_final: 0.8351 (tp30)
REVERT: H   98 GLN cc_start: 0.9423 (mm-40) cc_final: 0.8706 (mm-40)
  outliers start: 15
  outliers final: 8
  residues processed: 206
  average time/residue: 0.1182
  time to fit residues: 33.4130
Evaluate side-chains
  203 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 193
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain D residue  143 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   62 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 86 optimal weight:   10.0000
   chunk 51 optimal weight:    0.0060
   chunk 42 optimal weight:    0.7980
   chunk 76 optimal weight:    6.9990
   chunk 82 optimal weight:    6.9990
   chunk 83 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   chunk 58 optimal weight:    0.8980
   chunk 96 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.7396

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.066148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.046438 restraints weight = 50709.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 2.35
r_work: 0.2749 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8741
moved from start:          0.4054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12629  Z= 0.150
  Angle     :  0.580   7.468  18303  Z= 0.348
  Chirality :  0.034   0.164   2089
  Planarity :  0.004   0.038   1310
  Dihedral  : 31.470  89.019   4071
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 23.62 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.67 (0.31), residues: 730
  helix:  3.22 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.15 (0.42), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  72 
 TYR   0.022   0.002   TYR B  88 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.002   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (12629)
  covalent geometry    : angle       0.58024 (18303)
  hydrogen bonds       : bond        0.03639 (  754)
  hydrogen bonds       : angle       2.74858 ( 1895)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 210
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.9462 (tttm) cc_final: 0.9212 (tttm)
REVERT: A   55 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.8986 (mt0)
REVERT: A   59 GLU cc_start: 0.8893 (pm20) cc_final: 0.8506 (pm20)
REVERT: A   73 GLU cc_start: 0.8921 (tp30) cc_final: 0.8667 (tp30)
REVERT: A   81 ASP cc_start: 0.8893 (t0) cc_final: 0.8589 (t0)
REVERT: B   84 MET cc_start: 0.9064 (mmm) cc_final: 0.8640 (mmm)
REVERT: B   88 TYR cc_start: 0.9268 (m-10) cc_final: 0.8792 (m-10)
REVERT: C   65 GLU cc_start: 0.8657 (tp30) cc_final: 0.8233 (tp30)
REVERT: C  111 ASN cc_start: 0.8819 (p0) cc_final: 0.8523 (p0)
REVERT: D   94 GLU cc_start: 0.9158 (tp30) cc_final: 0.8423 (tp30)
REVERT: D   98 GLN cc_start: 0.9406 (mm-40) cc_final: 0.8744 (mm-40)
REVERT: D  143 LYS cc_start: 0.9694 (OUTLIER) cc_final: 0.9450 (tttm)
REVERT: E   53 LYS cc_start: 0.9439 (tttm) cc_final: 0.9140 (tttm)
REVERT: E   59 GLU cc_start: 0.8812 (pm20) cc_final: 0.8485 (pm20)
REVERT: F   84 MET cc_start: 0.9175 (mmm) cc_final: 0.8662 (mmm)
REVERT: G   21 LYS cc_start: 0.9386 (mmmt) cc_final: 0.8872 (tptm)
REVERT: G   65 GLU cc_start: 0.8716 (tp30) cc_final: 0.8449 (tp30)
REVERT: G   91 ASP cc_start: 0.7994 (t70) cc_final: 0.7628 (t70)
REVERT: H   94 GLU cc_start: 0.8957 (tp30) cc_final: 0.8295 (tp30)
REVERT: H   98 GLN cc_start: 0.9411 (mm-40) cc_final: 0.8716 (mm-40)
  outliers start: 14
  outliers final: 6
  residues processed: 215
  average time/residue: 0.1233
  time to fit residues: 36.5745
Evaluate side-chains
  209 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 201
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue  143 LYS
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue  121 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 74 optimal weight:    8.9990
   chunk 36 optimal weight:   10.0000
   chunk 64 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0970
   chunk 94 optimal weight:    4.9990
   chunk 86 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
D  86 ASN
E  68 GLN
H 132 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.064374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.044298 restraints weight = 50619.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 2.29
r_work: 0.2694 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8791
moved from start:          0.4136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12629  Z= 0.195
  Angle     :  0.608   7.533  18303  Z= 0.361
  Chirality :  0.035   0.174   2089
  Planarity :  0.004   0.036   1310
  Dihedral  : 31.737  89.376   4071
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 23.46 %
    Favored  : 74.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.59 (0.31), residues: 730
  helix:  3.15 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.19 (0.42), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 122 
 TYR   0.036   0.002   TYR B  88 
 PHE   0.009   0.001   PHE E  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (12629)
  covalent geometry    : angle       0.60838 (18303)
  hydrogen bonds       : bond        0.04428 (  754)
  hydrogen bonds       : angle       2.89437 ( 1895)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 195
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.9451 (tttm) cc_final: 0.9153 (tttm)
REVERT: A   55 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8854 (mt0)
REVERT: A   59 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8651 (pm20)
REVERT: A   81 ASP cc_start: 0.8867 (t0) cc_final: 0.8561 (t0)
REVERT: C   65 GLU cc_start: 0.8774 (tp30) cc_final: 0.8377 (tp30)
REVERT: C   91 ASP cc_start: 0.8411 (t70) cc_final: 0.8196 (t70)
REVERT: C  111 ASN cc_start: 0.8785 (p0) cc_final: 0.8450 (p0)
REVERT: D   94 GLU cc_start: 0.9154 (tp30) cc_final: 0.8416 (tp30)
REVERT: D   98 GLN cc_start: 0.9415 (mm-40) cc_final: 0.8732 (mm-40)
REVERT: D  106 TYR cc_start: 0.8313 (m-80) cc_final: 0.7708 (m-10)
REVERT: D  143 LYS cc_start: 0.9685 (OUTLIER) cc_final: 0.9333 (tttp)
REVERT: E   53 LYS cc_start: 0.9429 (tttm) cc_final: 0.9117 (tttm)
REVERT: E   59 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8591 (pm20)
REVERT: F   84 MET cc_start: 0.9188 (mmm) cc_final: 0.8578 (mmm)
REVERT: F   88 TYR cc_start: 0.9436 (m-10) cc_final: 0.8968 (m-10)
REVERT: G   21 LYS cc_start: 0.9390 (mmmt) cc_final: 0.8862 (tptm)
REVERT: G   65 GLU cc_start: 0.8782 (tp30) cc_final: 0.8511 (tp30)
REVERT: G   91 ASP cc_start: 0.8144 (t70) cc_final: 0.7858 (t70)
REVERT: H   94 GLU cc_start: 0.8975 (tp30) cc_final: 0.8332 (tp30)
REVERT: H   98 GLN cc_start: 0.9393 (mm-40) cc_final: 0.8707 (mm-40)
  outliers start: 13
  outliers final: 8
  residues processed: 203
  average time/residue: 0.1252
  time to fit residues: 34.7587
Evaluate side-chains
  205 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 193
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain D residue   86 ASN
Chi-restraints excluded: chain D residue  143 LYS
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue  121 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 80 optimal weight:    4.9990
   chunk 17 optimal weight:   10.0000
   chunk 79 optimal weight:    4.9990
   chunk 96 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 89 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 50 optimal weight:    0.8980
   chunk 98 optimal weight:    8.9990
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
C  25 GLN
D  86 ASN
E  68 GLN
** F  25 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 = 0.3485 r_free = 0.3485 target = 0.062536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.042664 restraints weight = 51367.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 2.32
r_work: 0.2641 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8833
moved from start:          0.4312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035  12629  Z= 0.269
  Angle     :  0.652   8.276  18303  Z= 0.386
  Chirality :  0.037   0.185   2089
  Planarity :  0.004   0.036   1310
  Dihedral  : 32.063  91.191   4071
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 23.62 %
    Favored  : 74.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.19 (0.31), residues: 730
  helix:  2.88 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.40 (0.42), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 122 
 TYR   0.040   0.003   TYR B  88 
 PHE   0.009   0.002   PHE H  93 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00604 (12629)
  covalent geometry    : angle       0.65232 (18303)
  hydrogen bonds       : bond        0.05632 (  754)
  hydrogen bonds       : angle       3.19327 ( 1895)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 188
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.9387 (tttm) cc_final: 0.9068 (tttm)
REVERT: A   55 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8847 (mt0)
REVERT: A   59 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8487 (pm20)
REVERT: A   81 ASP cc_start: 0.8954 (t0) cc_final: 0.8667 (t0)
REVERT: B   79 LYS cc_start: 0.9395 (ttmm) cc_final: 0.8704 (ttpt)
REVERT: C   42 GLU cc_start: 0.8700 (mp0) cc_final: 0.8498 (pm20)
REVERT: C   65 GLU cc_start: 0.8729 (tp30) cc_final: 0.8248 (tp30)
REVERT: C   91 ASP cc_start: 0.8431 (t70) cc_final: 0.8226 (t70)
REVERT: D   94 GLU cc_start: 0.9207 (tp30) cc_final: 0.8470 (tp30)
REVERT: D   98 GLN cc_start: 0.9432 (mm-40) cc_final: 0.8740 (mm-40)
REVERT: D  143 LYS cc_start: 0.9685 (OUTLIER) cc_final: 0.9279 (tttp)
REVERT: E   53 LYS cc_start: 0.9404 (tttm) cc_final: 0.9068 (tttm)
REVERT: F   84 MET cc_start: 0.9252 (mmm) cc_final: 0.8381 (mmm)
REVERT: F   88 TYR cc_start: 0.9475 (m-10) cc_final: 0.8887 (m-10)
REVERT: G   21 LYS cc_start: 0.9403 (mmmt) cc_final: 0.8860 (tptm)
REVERT: G   65 GLU cc_start: 0.8773 (tp30) cc_final: 0.8496 (tp30)
REVERT: G   91 ASP cc_start: 0.7933 (t70) cc_final: 0.7375 (t70)
REVERT: G   93 GLU cc_start: 0.9151 (mp0) cc_final: 0.8779 (pm20)
REVERT: H   94 GLU cc_start: 0.9042 (tp30) cc_final: 0.8376 (tp30)
REVERT: H   98 GLN cc_start: 0.9392 (mm-40) cc_final: 0.8687 (mm-40)
REVERT: H  136 GLU cc_start: 0.9334 (mm-30) cc_final: 0.9095 (mm-30)
  outliers start: 13
  outliers final: 9
  residues processed: 195
  average time/residue: 0.1313
  time to fit residues: 34.3044
Evaluate side-chains
  196 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 184
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   24 ASP
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain D residue  143 LYS
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue   62 ILE
Chi-restraints excluded: chain H residue  121 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:   10.0000
   chunk 82 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 84 optimal weight:    7.9990
   chunk 85 optimal weight:   10.0000
   chunk 50 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** D  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.064660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.044894 restraints weight = 50442.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 2.32
r_work: 0.2713 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8774
moved from start:          0.4458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12629  Z= 0.162
  Angle     :  0.609   8.403  18303  Z= 0.363
  Chirality :  0.035   0.172   2089
  Planarity :  0.004   0.036   1310
  Dihedral  : 31.621  87.093   4071
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 24.43 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.33 (0.31), residues: 730
  helix:  3.01 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.42 (0.42), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H 122 
 TYR   0.052   0.002   TYR B  88 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.002   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (12629)
  covalent geometry    : angle       0.60881 (18303)
  hydrogen bonds       : bond        0.03880 (  754)
  hydrogen bonds       : angle       2.86195 ( 1895)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2807.57 seconds
wall clock time: 48 minutes 37.85 seconds (2917.85 seconds total)