Starting phenix.real_space_refine
on Wed May 14 03:01:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jld_36393/05_2025/8jld_36393.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jld_36393/05_2025/8jld_36393.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jld_36393/05_2025/8jld_36393.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jld_36393/05_2025/8jld_36393.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jld_36393/05_2025/8jld_36393.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jld_36393/05_2025/8jld_36393.cif"
  }
  resolution = 2.48
  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=   0.006 sd=   0.049
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      10      5.16       5
     C    6540      2.51       5
     N    2221      2.21       5
     O    2784      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11844
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 782
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "B"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 826
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 724
          Classifications: {'peptide': 93}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 782
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "F"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 826
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 724
          Classifications: {'peptide': 93}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "I"
      Number of atoms: 2955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2955
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 6.96, per 1000 atoms: 0.59
  Number of scatterers: 11844
  At special positions: 0
  Unit cell: (118.72, 110.24, 116.6, 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      10     16.00
     P     289     15.00
     O    2784      8.00
     N    2221      7.00
     C    6540      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: 2.95
  Conformation dependent library (CDL) restraints added in 881.5 milliseconds
  

  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:  1384

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      74.0% alpha, 3.2% beta
      144 base pairs and 267 stacking pairs defined.
    Time for finding SS restraints: 6.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 4.005A  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
    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: 4.452A  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
    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: 4.063A  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 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
    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: 4.475A  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: 7.051A  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: 7.181A  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: 6.492A  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: 7.042A  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: 7.240A  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

    414 hydrogen bonds defined for protein.
    1218 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      367 hydrogen bonds
      730 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      267 stacking parallelities
  Total time for adding SS restraints: 4.95

  Time building geometry restraints manager: 3.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2608
        1.34 -     1.46: 4027
        1.46 -     1.58: 5413
        1.58 -     1.70: 577
        1.70 -     1.82: 20
  Bond restraints: 12645
  Sorted by residual:
  bond pdb=" N   LYS H  46 "
       pdb=" CA  LYS H  46 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.029 1.33e-02 5.65e+03 4.67e+00
  bond pdb=" N   ARG A 129 "
       pdb=" CA  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.459  1.483 -0.024 1.20e-02 6.94e+03 3.90e+00
  bond pdb=" N   GLU G  64 "
       pdb=" CA  GLU G  64 "
    ideal  model  delta    sigma   weight residual
    1.459  1.483 -0.023 1.19e-02 7.06e+03 3.82e+00
  bond pdb=" C3'  DC I  49 "
       pdb=" O3'  DC I  49 "
    ideal  model  delta    sigma   weight residual
    1.422  1.462 -0.040 3.00e-02 1.11e+03 1.74e+00
  bond pdb=" C3'  DC I  49 "
       pdb=" C2'  DC I  49 "
    ideal  model  delta    sigma   weight residual
    1.525  1.547 -0.022 2.00e-02 2.50e+03 1.24e+00
  ... (remaining 12640 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 17367
        1.54 -     3.09: 890
        3.09 -     4.63: 49
        4.63 -     6.17: 9
        6.17 -     7.72: 6
  Bond angle restraints: 18321
  Sorted by residual:
  angle pdb=" N   GLY H 104 "
        pdb=" CA  GLY H 104 "
        pdb=" C   GLY H 104 "
      ideal   model   delta    sigma   weight residual
     111.34  118.20   -6.86 1.82e+00 3.02e-01 1.42e+01
  angle pdb=" N   GLY D 104 "
        pdb=" CA  GLY D 104 "
        pdb=" C   GLY D 104 "
      ideal   model   delta    sigma   weight residual
     111.34  117.68   -6.34 1.82e+00 3.02e-01 1.21e+01
  angle pdb=" CG  ARG G  35 "
        pdb=" CD  ARG G  35 "
        pdb=" NE  ARG G  35 "
      ideal   model   delta    sigma   weight residual
     112.00  119.39   -7.39 2.20e+00 2.07e-01 1.13e+01
  angle pdb=" CA  MET D  59 "
        pdb=" CB  MET D  59 "
        pdb=" CG  MET D  59 "
      ideal   model   delta    sigma   weight residual
     114.10  120.04   -5.94 2.00e+00 2.50e-01 8.82e+00
  angle pdb=" CA  ARG A 129 "
        pdb=" C   ARG A 129 "
        pdb=" O   ARG A 129 "
      ideal   model   delta    sigma   weight residual
     120.90  117.85    3.05 1.07e+00 8.73e-01 8.15e+00
  ... (remaining 18316 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.29: 4330
       21.29 -    42.58: 1362
       42.58 -    63.88: 1107
       63.88 -    85.17: 46
       85.17 -   106.46: 4
  Dihedral angle restraints: 6849
    sinusoidal: 4697
      harmonic: 2152
  Sorted by residual:
  dihedral pdb=" CD  ARG A 129 "
           pdb=" NE  ARG A 129 "
           pdb=" CZ  ARG A 129 "
           pdb=" NH1 ARG A 129 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   60.23  -60.23     1      1.00e+01 1.00e-02 4.83e+01
  dihedral pdb=" CG  ARG C  71 "
           pdb=" CD  ARG C  71 "
           pdb=" NE  ARG C  71 "
           pdb=" CZ  ARG C  71 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   42.05   47.95     2      1.50e+01 4.44e-03 1.18e+01
  dihedral pdb=" CG  ARG E 131 "
           pdb=" CD  ARG E 131 "
           pdb=" NE  ARG E 131 "
           pdb=" CZ  ARG E 131 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.79   44.79     2      1.50e+01 4.44e-03 1.06e+01
  ... (remaining 6846 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1329
       0.033 -    0.067: 499
       0.067 -    0.100: 190
       0.100 -    0.133: 54
       0.133 -    0.166: 11
  Chirality restraints: 2083
  Sorted by residual:
  chirality pdb=" CA  GLU G  64 "
            pdb=" N   GLU G  64 "
            pdb=" C   GLU G  64 "
            pdb=" CB  GLU G  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.92e-01
  chirality pdb=" CA  ILE B  29 "
            pdb=" N   ILE B  29 "
            pdb=" C   ILE B  29 "
            pdb=" CB  ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.51e-01
  chirality pdb=" C3'  DG I  54 "
            pdb=" C4'  DG I  54 "
            pdb=" O3'  DG I  54 "
            pdb=" C2'  DG I  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.81    0.15 2.00e-01 2.50e+01 5.37e-01
  ... (remaining 2080 not shown)

  Planarity restraints: 1316
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 129 "    0.946 9.50e-02 1.11e+02   4.24e-01 1.09e+02
        pdb=" NE  ARG A 129 "   -0.057 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 129 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 129 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 129 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  95 "    0.422 9.50e-02 1.11e+02   1.89e-01 2.19e+01
        pdb=" NE  ARG B  95 "   -0.025 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  95 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  95 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  95 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  19 "    0.016 2.00e-02 2.50e+03   1.71e-02 6.58e+00
        pdb=" N1   DC J  19 "   -0.039 2.00e-02 2.50e+03
        pdb=" C2   DC J  19 "    0.028 2.00e-02 2.50e+03
        pdb=" O2   DC J  19 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3   DC J  19 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DC J  19 "    0.000 2.00e-02 2.50e+03
        pdb=" N4   DC J  19 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DC J  19 "    0.004 2.00e-02 2.50e+03
        pdb=" C6   DC J  19 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1313 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 19
        2.53 -     3.12: 7925
        3.12 -     3.72: 20865
        3.72 -     4.31: 30867
        4.31 -     4.90: 43915
  Nonbonded interactions: 103591
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  57 "
            pdb=" OE1 GLU A  59 "
     model   vdw
     1.941 3.040
  nonbonded pdb=" O2   DC I -23 "
            pdb=" N2   DG J  23 "
     model   vdw
     2.114 2.496
  nonbonded pdb=" NH1 ARG C  11 "
            pdb=" O2   DT I -42 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" OH  TYR C  39 "
            pdb=" OE1 GLU D  71 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OH  TYR G  39 "
            pdb=" OE2 GLU H  71 "
     model   vdw
     2.297 3.040
  ... (remaining 103586 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:             0.320
  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:          0.470
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     33.040
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12645  Z= 0.190
  Angle     :  0.706   7.717  18321  Z= 0.442
  Chirality :  0.042   0.166   2083
  Planarity :  0.014   0.424   1316
  Dihedral  : 29.740 106.461   5465
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 17.37 %
    Favored  : 82.31 %
  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:  0.65 (0.27), residues: 730
  helix:  0.79 (0.20), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.35 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.011   0.002   TYR F  51 
 ARG   0.012   0.001   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07192 (  781)
  hydrogen bonds       : angle       3.35582 ( 1948)
  covalent geometry    : bond        0.00389 (12645)
  covalent geometry    : angle       0.70559 (18321)

*********************** 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
  165 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 163
  time to evaluate  : 0.905 
Fit side-chains
REVERT: G   73 ASN cc_start: 0.8425 (t0) cc_final: 0.8170 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 163
  average time/residue: 1.9877
  time to fit residues: 340.0946
Evaluate side-chains
  151 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   89 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 74 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   chunk 39 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 57 optimal weight:    7.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    2.4584

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  67 ASN
F  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.097917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.085075 restraints weight = 18296.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 0.98
r_work: 0.3093 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.1447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034  12645  Z= 0.253
  Angle     :  0.618   5.661  18321  Z= 0.377
  Chirality :  0.038   0.129   2083
  Planarity :  0.005   0.032   1316
  Dihedral  : 30.834 100.414   4005
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 17.21 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.01 (0.31), residues: 730
  helix:  2.73 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.18 (0.39), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.001   HIS B  75 
 PHE   0.009   0.002   PHE A  67 
 TYR   0.010   0.002   TYR D 121 
 ARG   0.007   0.001   ARG A  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05541 (  781)
  hydrogen bonds       : angle       2.98146 ( 1948)
  covalent geometry    : bond        0.00574 (12645)
  covalent geometry    : angle       0.61813 (18321)

*********************** 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
  185 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 166
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 ARG cc_start: 0.8572 (mtp-110) cc_final: 0.8280 (ttm170)
REVERT: A   58 THR cc_start: 0.8927 (p) cc_final: 0.8643 (t)
REVERT: A   83 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8234 (mtt90)
REVERT: B   93 GLN cc_start: 0.8367 (mt0) cc_final: 0.8006 (mp10)
REVERT: C   73 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8152 (t160)
REVERT: D   79 ARG cc_start: 0.8757 (ttp-170) cc_final: 0.8522 (ttp-170)
REVERT: E   40 ARG cc_start: 0.8392 (mtp85) cc_final: 0.8117 (mtp85)
REVERT: E   83 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7844 (mtm180)
REVERT: F   84 MET cc_start: 0.8661 (mmm) cc_final: 0.8437 (mmp)
REVERT: G   17 ARG cc_start: 0.8715 (mtp180) cc_final: 0.8443 (mtp180)
REVERT: G   73 ASN cc_start: 0.8482 (t0) cc_final: 0.8207 (t0)
REVERT: G   91 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.3689 (tp30)
  outliers start: 19
  outliers final: 7
  residues processed: 171
  average time/residue: 1.9420
  time to fit residues: 348.7020
Evaluate side-chains
  173 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 162
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue   83 ARG
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 84 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 59 optimal weight:    0.4980
   chunk 97 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
D  47 GLN
D  63 ASN
D  95 GLN
F  27 GLN
F  93 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.099455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.086630 restraints weight = 18414.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 0.97
r_work: 0.3114 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  12645  Z= 0.174
  Angle     :  0.578   7.989  18321  Z= 0.358
  Chirality :  0.035   0.127   2083
  Planarity :  0.004   0.033   1316
  Dihedral  : 30.828  99.891   4003
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 18.18 %
    Favored  : 79.06 %
  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:  3.22 (0.30), residues: 730
  helix:  2.93 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.23 (0.37), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.011   0.001   TYR D  83 
 ARG   0.008   0.001   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05120 (  781)
  hydrogen bonds       : angle       2.84832 ( 1948)
  covalent geometry    : bond        0.00375 (12645)
  covalent geometry    : angle       0.57772 (18321)

*********************** 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
  178 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 161
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 ARG cc_start: 0.8527 (mtp-110) cc_final: 0.8283 (ttm170)
REVERT: A  129 ARG cc_start: 0.8304 (mmm160) cc_final: 0.7726 (tpt90)
REVERT: B   35 ARG cc_start: 0.8570 (mtp85) cc_final: 0.8275 (mtp85)
REVERT: C   73 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8129 (t160)
REVERT: C   77 ARG cc_start: 0.9098 (mtm-85) cc_final: 0.8878 (mtt90)
REVERT: C   91 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.3456 (tp30)
REVERT: C   99 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7706 (mtm110)
REVERT: D   79 ARG cc_start: 0.8732 (ttp-170) cc_final: 0.8494 (ttp-170)
REVERT: G   73 ASN cc_start: 0.8429 (t0) cc_final: 0.8174 (t0)
REVERT: G   91 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.3629 (tp30)
  outliers start: 17
  outliers final: 7
  residues processed: 166
  average time/residue: 2.0107
  time to fit residues: 350.8693
Evaluate side-chains
  169 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 158
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue   99 ARG
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   91 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 93 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 88 optimal weight:    5.9990
   chunk 94 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
C 104 GLN
D  84 ASN
E  76 GLN
F  27 GLN
F  93 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.095225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.082691 restraints weight = 18480.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 0.99
r_work: 0.3056 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041  12645  Z= 0.299
  Angle     :  0.629   5.900  18321  Z= 0.384
  Chirality :  0.040   0.131   2083
  Planarity :  0.005   0.035   1316
  Dihedral  : 30.542  98.168   4003
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 17.53 %
    Favored  : 79.06 %
  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 (0.30), residues: 730
  helix:  2.68 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.36 (0.37), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS B  75 
 PHE   0.011   0.002   PHE A  67 
 TYR   0.014   0.002   TYR H 121 
 ARG   0.005   0.001   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06009 (  781)
  hydrogen bonds       : angle       2.96877 ( 1948)
  covalent geometry    : bond        0.00685 (12645)
  covalent geometry    : angle       0.62937 (18321)

*********************** 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
  179 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 158
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
REVERT: B   35 ARG cc_start: 0.8607 (mtp85) cc_final: 0.8295 (mtp85)
REVERT: B   93 GLN cc_start: 0.8459 (mt0) cc_final: 0.8145 (mp10)
REVERT: C   11 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7366 (pmm-80)
REVERT: C   73 ASN cc_start: 0.8565 (t0) cc_final: 0.8218 (t160)
REVERT: C   91 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.5711 (mp0)
REVERT: G   73 ASN cc_start: 0.8499 (t0) cc_final: 0.8200 (t0)
REVERT: G   91 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.3630 (tp30)
  outliers start: 21
  outliers final: 8
  residues processed: 166
  average time/residue: 1.9439
  time to fit residues: 339.4186
Evaluate side-chains
  165 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 154
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain C residue   11 ARG
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain D residue   33 ARG
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue   78 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0030
   chunk 21 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
F  27 GLN
F  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.097171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.084677 restraints weight = 18318.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 0.97
r_work: 0.3092 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12645  Z= 0.167
  Angle     :  0.592   8.832  18321  Z= 0.365
  Chirality :  0.035   0.130   2083
  Planarity :  0.004   0.032   1316
  Dihedral  : 30.573  97.584   4003
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 18.51 %
    Favored  : 78.57 %
  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:  3.12 (0.30), residues: 730
  helix:  2.85 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.25 (0.38), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.008   0.001   PHE D  70 
 TYR   0.013   0.001   TYR F  88 
 ARG   0.004   0.001   ARG E  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05239 (  781)
  hydrogen bonds       : angle       2.86096 ( 1948)
  covalent geometry    : bond        0.00353 (12645)
  covalent geometry    : angle       0.59172 (18321)

*********************** 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
  180 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 162
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8291 (mmm160) cc_final: 0.7810 (tpt90)
REVERT: B   35 ARG cc_start: 0.8574 (mtp85) cc_final: 0.8291 (mtp85)
REVERT: B   93 GLN cc_start: 0.8408 (mt0) cc_final: 0.7939 (mm-40)
REVERT: C   73 ASN cc_start: 0.8526 (t0) cc_final: 0.8179 (t160)
REVERT: C   91 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.5605 (mp0)
REVERT: D   79 ARG cc_start: 0.8716 (ttp-170) cc_final: 0.8497 (ttp-170)
REVERT: E  129 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7850 (ttp80)
REVERT: F   68 ASP cc_start: 0.8548 (m-30) cc_final: 0.8337 (m-30)
REVERT: G   73 ASN cc_start: 0.8429 (t0) cc_final: 0.8172 (t0)
REVERT: G   91 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.3574 (tp30)
  outliers start: 18
  outliers final: 6
  residues processed: 171
  average time/residue: 1.8774
  time to fit residues: 337.5851
Evaluate side-chains
  166 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 157
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue   99 ARG
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   78 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   chunk 21 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 92 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
F  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.097398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.084905 restraints weight = 18452.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 0.98
r_work: 0.3099 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12645  Z= 0.178
  Angle     :  0.575   5.441  18321  Z= 0.358
  Chirality :  0.035   0.133   2083
  Planarity :  0.004   0.033   1316
  Dihedral  : 30.512  97.596   4003
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.81 %
    Favored  : 77.92 %
  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:  3.24 (0.30), residues: 730
  helix:  2.93 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.20 (0.38), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.011   0.001   TYR F  88 
 ARG   0.005   0.000   ARG E  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05145 (  781)
  hydrogen bonds       : angle       2.80951 ( 1948)
  covalent geometry    : bond        0.00386 (12645)
  covalent geometry    : angle       0.57548 (18321)

*********************** 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
  173 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 159
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8291 (mmm160) cc_final: 0.7820 (tpt90)
REVERT: B   35 ARG cc_start: 0.8589 (mtp85) cc_final: 0.8332 (mtp85)
REVERT: B   93 GLN cc_start: 0.8428 (mt0) cc_final: 0.8064 (mm-40)
REVERT: C   11 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7582 (pmm-80)
REVERT: C   73 ASN cc_start: 0.8525 (t0) cc_final: 0.8192 (t160)
REVERT: C   91 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.5740 (mp0)
REVERT: E  129 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7848 (ttp80)
REVERT: G   73 ASN cc_start: 0.8432 (t0) cc_final: 0.8164 (t0)
REVERT: G   91 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.3556 (tp30)
  outliers start: 14
  outliers final: 8
  residues processed: 167
  average time/residue: 1.8662
  time to fit residues: 327.8413
Evaluate side-chains
  170 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 158
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain C residue   11 ARG
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue   99 ARG
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain E residue  129 ARG
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue   78 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 52 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    7.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A 108 ASN
E  68 GLN
F  27 GLN
H  47 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.098488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.085978 restraints weight = 18406.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 0.98
r_work: 0.3120 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  12645  Z= 0.163
  Angle     :  0.570  11.497  18321  Z= 0.352
  Chirality :  0.034   0.139   2083
  Planarity :  0.004   0.063   1316
  Dihedral  : 30.470  96.420   4003
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 20.29 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.34 (0.30), residues: 730
  helix:  3.00 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.14 (0.39), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.014   0.001   TYR F  88 
 ARG   0.010   0.000   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04858 (  781)
  hydrogen bonds       : angle       2.72642 ( 1948)
  covalent geometry    : bond        0.00345 (12645)
  covalent geometry    : angle       0.56959 (18321)

*********************** 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
  179 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 164
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8282 (mmm160) cc_final: 0.7829 (tpt90)
REVERT: B   35 ARG cc_start: 0.8581 (mtp85) cc_final: 0.8332 (mtp85)
REVERT: B   93 GLN cc_start: 0.8411 (mt0) cc_final: 0.8133 (mm-40)
REVERT: C   11 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7561 (pmm-80)
REVERT: C   73 ASN cc_start: 0.8512 (t0) cc_final: 0.8177 (t160)
REVERT: C   91 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.5770 (mp0)
REVERT: E   53 ARG cc_start: 0.8679 (tmm-80) cc_final: 0.8467 (ttt-90)
REVERT: E   63 ARG cc_start: 0.8449 (mmp80) cc_final: 0.8223 (mmp80)
REVERT: G   73 ASN cc_start: 0.8419 (t0) cc_final: 0.8141 (t0)
REVERT: G   91 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.3451 (tp30)
  outliers start: 15
  outliers final: 8
  residues processed: 171
  average time/residue: 1.9607
  time to fit residues: 351.9959
Evaluate side-chains
  173 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 162
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain C residue   11 ARG
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue   99 ARG
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue   78 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 67 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   chunk 88 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
D  84 ASN
F  27 GLN
H  47 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.097707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.085192 restraints weight = 18400.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 0.97
r_work: 0.3104 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.2138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028  12645  Z= 0.210
  Angle     :  0.578   8.103  18321  Z= 0.356
  Chirality :  0.036   0.133   2083
  Planarity :  0.004   0.033   1316
  Dihedral  : 30.335  95.275   4003
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 20.78 %
    Favored  : 76.79 %
  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:  3.28 (0.30), residues: 730
  helix:  2.95 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.17 (0.39), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.009   0.001   PHE D  70 
 TYR   0.012   0.001   TYR H 121 
 ARG   0.004   0.000   ARG F  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04995 (  781)
  hydrogen bonds       : angle       2.75677 ( 1948)
  covalent geometry    : bond        0.00468 (12645)
  covalent geometry    : angle       0.57781 (18321)

*********************** 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
  174 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 159
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
REVERT: B   35 ARG cc_start: 0.8600 (mtp85) cc_final: 0.8327 (mtp85)
REVERT: B   93 GLN cc_start: 0.8433 (mt0) cc_final: 0.8152 (mm-40)
REVERT: C   11 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7513 (pmm-80)
REVERT: C   73 ASN cc_start: 0.8542 (t0) cc_final: 0.8158 (t160)
REVERT: C   91 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.5728 (mp0)
REVERT: G   73 ASN cc_start: 0.8442 (t0) cc_final: 0.8158 (t0)
REVERT: G   91 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.3531 (tp30)
  outliers start: 15
  outliers final: 11
  residues processed: 166
  average time/residue: 1.9007
  time to fit residues: 331.4151
Evaluate side-chains
  171 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 157
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain C residue   11 ARG
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue   99 ARG
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue  123 SER
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue   78 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 35 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
D  84 ASN
F  27 GLN
H  47 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.098012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.085526 restraints weight = 18386.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 0.97
r_work: 0.3110 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  12645  Z= 0.185
  Angle     :  0.574   7.359  18321  Z= 0.354
  Chirality :  0.035   0.131   2083
  Planarity :  0.004   0.033   1316
  Dihedral  : 30.345  95.261   4003
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 20.29 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.31 (0.30), residues: 730
  helix:  2.98 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.15 (0.39), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.011   0.001   TYR F  88 
 ARG   0.007   0.000   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04913 (  781)
  hydrogen bonds       : angle       2.75275 ( 1948)
  covalent geometry    : bond        0.00403 (12645)
  covalent geometry    : angle       0.57393 (18321)

*********************** 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
  175 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8240 (mtt90)
REVERT: A  129 ARG cc_start: 0.8269 (mmm160) cc_final: 0.7828 (tpt90)
REVERT: B   35 ARG cc_start: 0.8598 (mtp85) cc_final: 0.8333 (mtp85)
REVERT: B   93 GLN cc_start: 0.8418 (mt0) cc_final: 0.8193 (mm-40)
REVERT: C   11 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7505 (pmm-80)
REVERT: C   73 ASN cc_start: 0.8534 (t0) cc_final: 0.8149 (t160)
REVERT: C   91 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.5725 (mp0)
REVERT: E   63 ARG cc_start: 0.8460 (mmp80) cc_final: 0.8209 (mmp80)
REVERT: G   73 ASN cc_start: 0.8431 (t0) cc_final: 0.8145 (t0)
REVERT: G   91 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.3465 (tp30)
  outliers start: 16
  outliers final: 9
  residues processed: 167
  average time/residue: 1.9307
  time to fit residues: 338.2981
Evaluate side-chains
  170 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 157
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain C residue   11 ARG
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue   99 ARG
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue   78 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 80 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 45 optimal weight:    0.7980
   chunk 73 optimal weight:    5.9990
   chunk 55 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
D  84 ASN
F  27 GLN
H  47 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.098333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.085868 restraints weight = 18276.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 0.97
r_work: 0.3115 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  12645  Z= 0.171
  Angle     :  0.572   7.575  18321  Z= 0.353
  Chirality :  0.034   0.130   2083
  Planarity :  0.004   0.032   1316
  Dihedral  : 30.353  95.154   4003
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 20.62 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.33 (0.30), residues: 730
  helix:  2.99 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.13 (0.39), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.012   0.001   TYR F  88 
 ARG   0.004   0.000   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04813 (  781)
  hydrogen bonds       : angle       2.74980 ( 1948)
  covalent geometry    : bond        0.00366 (12645)
  covalent geometry    : angle       0.57174 (18321)

********************** 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
  173 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 159
  time to evaluate  : 0.810 
Fit side-chains
REVERT: A   83 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8242 (mtt90)
REVERT: A  129 ARG cc_start: 0.8265 (mmm160) cc_final: 0.7828 (tpt90)
REVERT: B   35 ARG cc_start: 0.8595 (mtp85) cc_final: 0.8352 (mtp85)
REVERT: B   93 GLN cc_start: 0.8401 (mt0) cc_final: 0.8173 (mm-40)
REVERT: C   11 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7494 (pmm-80)
REVERT: C   73 ASN cc_start: 0.8541 (t0) cc_final: 0.8166 (t160)
REVERT: C   91 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.5734 (mp0)
REVERT: E   63 ARG cc_start: 0.8448 (mmp80) cc_final: 0.8197 (mmp80)
REVERT: G   73 ASN cc_start: 0.8427 (t0) cc_final: 0.8139 (t0)
REVERT: G   91 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.3453 (tp30)
  outliers start: 14
  outliers final: 9
  residues processed: 167
  average time/residue: 1.9733
  time to fit residues: 345.6928
Evaluate side-chains
  172 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 159
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   83 ARG
Chi-restraints excluded: chain C residue   11 ARG
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue   99 ARG
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain G residue   36 LYS
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue   78 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 80 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0970
   chunk 68 optimal weight:    0.6980
   chunk 91 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   chunk 17 optimal weight:    0.4980
   chunk 55 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
D  84 ASN
F  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.098586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.086127 restraints weight = 18284.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 0.96
r_work: 0.3122 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12645  Z= 0.159
  Angle     :  0.566   7.049  18321  Z= 0.350
  Chirality :  0.034   0.131   2083
  Planarity :  0.004   0.037   1316
  Dihedral  : 30.354  95.189   4003
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 20.62 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.37 (0.30), residues: 730
  helix:  3.02 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.13 (0.39), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.011   0.001   TYR F  88 
 ARG   0.006   0.000   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04745 (  781)
  hydrogen bonds       : angle       2.73477 ( 1948)
  covalent geometry    : bond        0.00336 (12645)
  covalent geometry    : angle       0.56576 (18321)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9119.38 seconds
wall clock time: 156 minutes 56.23 seconds (9416.23 seconds total)