Starting phenix.real_space_refine
on Tue Jul 29 11:29:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jld_36393/07_2025/8jld_36393.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jld_36393/07_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_36393/07_2025/8jld_36393.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jld_36393/07_2025/8jld_36393.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jld_36393/07_2025/8jld_36393.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jld_36393/07_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-5711/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: 7.44, per 1000 atoms: 0.63
  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: 3.18
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 6.89
  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: 5.21

  Time building geometry restraints manager: 3.83 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:             0.410
  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:          0.540
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     36.150
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:14.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.010
-------------------------------------------------------------------------------
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  : 0.826 
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: 1.9941
  time to fit residues: 341.1227
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  : 0.871 
-------------------------------------------------------------------------------
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 = 38)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.085079 restraints weight = 18296.839|
|-----------------------------------------------------------------------------|
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  : 0.918 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 ARG cc_start: 0.8571 (mtp-110) cc_final: 0.8278 (ttm170)
REVERT: A   58 THR cc_start: 0.8927 (p) cc_final: 0.8642 (t)
REVERT: A   83 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8233 (mtt90)
REVERT: B   93 GLN cc_start: 0.8360 (mt0) cc_final: 0.7999 (mp10)
REVERT: C   73 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8146 (t160)
REVERT: D   79 ARG cc_start: 0.8751 (ttp-170) cc_final: 0.8515 (ttp-170)
REVERT: E   40 ARG cc_start: 0.8392 (mtp85) cc_final: 0.8115 (mtp85)
REVERT: E   83 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7839 (mtm180)
REVERT: F   84 MET cc_start: 0.8663 (mmm) cc_final: 0.8438 (mmp)
REVERT: G   17 ARG cc_start: 0.8714 (mtp180) cc_final: 0.8443 (mtp180)
REVERT: G   73 ASN cc_start: 0.8475 (t0) cc_final: 0.8201 (t0)
REVERT: G   91 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.3692 (tp30)
  outliers start: 19
  outliers final: 7
  residues processed: 171
  average time/residue: 1.9806
  time to fit residues: 355.5910
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  : 1.346 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 88 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 97 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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  95 GLN
F  27 GLN
F  93 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.099561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.086750 restraints weight = 18433.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 0.98
r_work: 0.3118 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  12645  Z= 0.194
  Angle     :  0.572   5.359  18321  Z= 0.355
  Chirality :  0.035   0.125   2083
  Planarity :  0.004   0.034   1316
  Dihedral  : 30.727  98.216   4003
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 18.18 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.29 (0.30), residues: 730
  helix:  2.97 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.19 (0.38), 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   0.012   0.001   TYR D  83 
 ARG   0.006   0.001   ARG A  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05035 (  781)
  hydrogen bonds       : angle       2.82243 ( 1948)
  covalent geometry    : bond        0.00430 (12645)
  covalent geometry    : angle       0.57154 (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
  176 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 ARG cc_start: 0.8570 (mtp-110) cc_final: 0.8334 (ttm170)
REVERT: B   35 ARG cc_start: 0.8579 (mtp85) cc_final: 0.8262 (mtp85)
REVERT: C   73 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8153 (t160)
REVERT: C   91 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.3676 (tp30)
REVERT: C   99 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7721 (mtm110)
REVERT: E   83 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7840 (mtm180)
REVERT: G   73 ASN cc_start: 0.8460 (t0) cc_final: 0.8173 (t0)
REVERT: G   91 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.3637 (tp30)
  outliers start: 18
  outliers final: 7
  residues processed: 166
  average time/residue: 2.3715
  time to fit residues: 413.6536
Evaluate side-chains
  166 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 154
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
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   83 ARG
Chi-restraints excluded: chain F residue   77 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
Chi-restraints excluded: chain H residue  123 SER
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:    6.9990
   chunk 88 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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
D  63 ASN
E  76 GLN
F  93 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.095488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.082843 restraints weight = 18471.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 0.99
r_work: 0.3053 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044  12645  Z= 0.302
  Angle     :  0.633   7.579  18321  Z= 0.386
  Chirality :  0.041   0.131   2083
  Planarity :  0.005   0.034   1316
  Dihedral  : 30.547  97.915   4003
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 16.88 %
    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:  2.90 (0.30), residues: 730
  helix:  2.67 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.30 (0.38), 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   0.013   0.002   TYR F  88 
 ARG   0.004   0.001   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05984 (  781)
  hydrogen bonds       : angle       2.96986 ( 1948)
  covalent geometry    : bond        0.00690 (12645)
  covalent geometry    : angle       0.63309 (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
  176 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 155
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
REVERT: B   35 ARG cc_start: 0.8611 (mtp85) cc_final: 0.8303 (mtp85)
REVERT: B   93 GLN cc_start: 0.8444 (mt0) cc_final: 0.8120 (mp10)
REVERT: C   11 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7493 (pmm-80)
REVERT: C   73 ASN cc_start: 0.8566 (t0) cc_final: 0.8221 (t160)
REVERT: C   91 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.5633 (mp0)
REVERT: E   83 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7957 (mtm180)
REVERT: F   93 GLN cc_start: 0.8575 (mt0) cc_final: 0.8314 (mt0)
REVERT: G   73 ASN cc_start: 0.8486 (t0) cc_final: 0.8217 (t0)
REVERT: G   91 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.3658 (tp30)
  outliers start: 21
  outliers final: 8
  residues processed: 164
  average time/residue: 2.0088
  time to fit residues: 346.1703
Evaluate side-chains
  162 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain C residue   11 ARG
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain E residue   83 ARG
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:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 63 optimal weight:    7.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
E  76 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.097264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.084619 restraints weight = 18294.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 0.97
r_work: 0.3091 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12645  Z= 0.176
  Angle     :  0.594   5.701  18321  Z= 0.367
  Chirality :  0.035   0.131   2083
  Planarity :  0.004   0.054   1316
  Dihedral  : 30.591  97.565   4003
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 18.83 %
    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:  3.11 (0.30), residues: 730
  helix:  2.84 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.26 (0.38), 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   0.010   0.001   TYR F  88 
 ARG   0.005   0.001   ARG C  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05311 (  781)
  hydrogen bonds       : angle       2.87232 ( 1948)
  covalent geometry    : bond        0.00378 (12645)
  covalent geometry    : angle       0.59439 (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
  175 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 THR cc_start: 0.9077 (m) cc_final: 0.8876 (m)
REVERT: A  129 ARG cc_start: 0.8282 (mmm160) cc_final: 0.7803 (tpt90)
REVERT: B   35 ARG cc_start: 0.8582 (mtp85) cc_final: 0.8307 (mtp85)
REVERT: B   93 GLN cc_start: 0.8359 (mt0) cc_final: 0.7890 (mm-40)
REVERT: C   11 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7366 (pmm-80)
REVERT: C   73 ASN cc_start: 0.8551 (t0) cc_final: 0.8204 (t160)
REVERT: C   91 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.5645 (mp0)
REVERT: E  129 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7879 (ttp80)
REVERT: F   93 GLN cc_start: 0.8492 (mt0) cc_final: 0.8239 (mt0)
REVERT: G   73 ASN cc_start: 0.8452 (t0) cc_final: 0.8198 (t0)
REVERT: G   91 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.3602 (tp30)
  outliers start: 16
  outliers final: 8
  residues processed: 167
  average time/residue: 1.9128
  time to fit residues: 335.8977
Evaluate side-chains
  168 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 156
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
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   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:    0.9980
   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:    0.7980
   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:    0.8780

-------------------------------------------------------------------------------
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 = 0.3410 r_free = 0.3410 target = 0.097776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.085135 restraints weight = 18430.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 0.99
r_work: 0.3102 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.1969

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= 0.177
  Angle     :  0.583  11.540  18321  Z= 0.359
  Chirality :  0.035   0.138   2083
  Planarity :  0.004   0.032   1316
  Dihedral  : 30.532  97.314   4003
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 19.64 %
    Favored  : 77.76 %
  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:  3.17 (0.30), residues: 730
  helix:  2.90 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.27 (0.38), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.015   0.001   TYR F  88 
 ARG   0.004   0.000   ARG E  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05123 (  781)
  hydrogen bonds       : angle       2.80087 ( 1948)
  covalent geometry    : bond        0.00383 (12645)
  covalent geometry    : angle       0.58321 (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
  178 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 162
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8267 (mmm160) cc_final: 0.7806 (tpt90)
REVERT: B   35 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8313 (mtp85)
REVERT: B   93 GLN cc_start: 0.8418 (mt0) cc_final: 0.8073 (mm-40)
REVERT: C   73 ASN cc_start: 0.8536 (t0) cc_final: 0.8208 (t160)
REVERT: C   91 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.5751 (mp0)
REVERT: G   73 ASN cc_start: 0.8447 (t0) cc_final: 0.8173 (t0)
REVERT: G   91 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.3533 (tp30)
  outliers start: 16
  outliers final: 9
  residues processed: 169
  average time/residue: 2.1529
  time to fit residues: 383.9548
Evaluate side-chains
  170 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 159
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
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   91 GLU
Chi-restraints excluded: chain C residue   99 ARG
Chi-restraints excluded: chain C residue  108 LEU
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   78 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 73 optimal weight:    5.9990
   chunk 48 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0980
   chunk 52 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    7.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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
D  84 ASN
F  27 GLN
F  93 GLN
H  47 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.098866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.086209 restraints weight = 18404.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 0.98
r_work: 0.3117 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  12645  Z= 0.158
  Angle     :  0.572  10.124  18321  Z= 0.353
  Chirality :  0.034   0.137   2083
  Planarity :  0.004   0.050   1316
  Dihedral  : 30.525  96.460   4003
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 19.97 %
    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:  3.35 (0.30), residues: 730
  helix:  3.01 (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   0.010   0.001   TYR F  88 
 ARG   0.005   0.000   ARG E  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04841 (  781)
  hydrogen bonds       : angle       2.74794 ( 1948)
  covalent geometry    : bond        0.00333 (12645)
  covalent geometry    : angle       0.57151 (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
  180 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 162
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8232 (mtt90)
REVERT: A  129 ARG cc_start: 0.8257 (mmm160) cc_final: 0.7808 (tpt90)
REVERT: B   35 ARG cc_start: 0.8576 (mtp85) cc_final: 0.8312 (mtp85)
REVERT: B   93 GLN cc_start: 0.8372 (mt0) cc_final: 0.8097 (mm-40)
REVERT: C   11 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7591 (pmm-80)
REVERT: C   73 ASN cc_start: 0.8527 (t0) cc_final: 0.8179 (t160)
REVERT: C   91 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.5760 (mp0)
REVERT: E   53 ARG cc_start: 0.8698 (tmm-80) cc_final: 0.8479 (ttt-90)
REVERT: G   73 ASN cc_start: 0.8435 (t0) cc_final: 0.8166 (t0)
REVERT: G   91 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.3502 (tp30)
  outliers start: 18
  outliers final: 7
  residues processed: 173
  average time/residue: 2.8526
  time to fit residues: 520.0427
Evaluate side-chains
  171 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 160
  time to evaluate  : 1.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
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 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:    0.7980
   chunk 67 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 17 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 88 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
D  84 ASN
F  27 GLN
F  93 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.097770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.085260 restraints weight = 18370.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 0.98
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: 0.8446
moved from start:          0.2108

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= 0.213
  Angle     :  0.584   9.925  18321  Z= 0.358
  Chirality :  0.036   0.131   2083
  Planarity :  0.004   0.033   1316
  Dihedral  : 30.357  95.403   4003
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 20.13 %
    Favored  : 77.60 %
  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:  2.96 (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   0.006   0.001   HIS B  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.013   0.001   TYR F  88 
 ARG   0.004   0.000   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05018 (  781)
  hydrogen bonds       : angle       2.76195 ( 1948)
  covalent geometry    : bond        0.00475 (12645)
  covalent geometry    : angle       0.58388 (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
  172 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 158
  time to evaluate  : 2.819 
Fit side-chains
REVERT: A   83 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8233 (mtt90)
REVERT: A  129 ARG cc_start: 0.8269 (mmm160) cc_final: 0.7830 (tpt90)
REVERT: B   35 ARG cc_start: 0.8594 (mtp85) cc_final: 0.8339 (mtp85)
REVERT: B   93 GLN cc_start: 0.8420 (mt0) cc_final: 0.8147 (mm-40)
REVERT: C   11 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7528 (pmm-80)
REVERT: C   73 ASN cc_start: 0.8550 (t0) cc_final: 0.8197 (t160)
REVERT: C   91 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.5821 (mp0)
REVERT: F   93 GLN cc_start: 0.8470 (mt0) cc_final: 0.8251 (mt0)
REVERT: G   73 ASN cc_start: 0.8426 (t0) cc_final: 0.8136 (t0)
REVERT: G   91 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.3537 (tp30)
  outliers start: 14
  outliers final: 9
  residues processed: 166
  average time/residue: 3.1433
  time to fit residues: 548.8014
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  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
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 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   91 GLU
Chi-restraints excluded: chain H residue   63 ASN
Chi-restraints excluded: chain H residue   78 SER
Chi-restraints excluded: chain H residue  120 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
D  84 ASN
F  27 GLN
H  47 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.098165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.085668 restraints weight = 18375.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 0.96
r_work: 0.3112 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12645  Z= 0.180
  Angle     :  0.577   9.375  18321  Z= 0.355
  Chirality :  0.035   0.131   2083
  Planarity :  0.004   0.032   1316
  Dihedral  : 30.377  95.348   4003
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 20.45 %
    Favored  : 76.95 %
  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 : -0.16 (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   0.009   0.001   TYR F  88 
 ARG   0.004   0.000   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04878 (  781)
  hydrogen bonds       : angle       2.74378 ( 1948)
  covalent geometry    : bond        0.00393 (12645)
  covalent geometry    : angle       0.57733 (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
  172 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 1.731 
Fit side-chains
REVERT: A   83 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8238 (mtt90)
REVERT: A  129 ARG cc_start: 0.8258 (mmm160) cc_final: 0.7828 (tpt90)
REVERT: B   35 ARG cc_start: 0.8592 (mtp85) cc_final: 0.8331 (mtp85)
REVERT: B   93 GLN cc_start: 0.8408 (mt0) cc_final: 0.8193 (mm-40)
REVERT: C   11 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7543 (pmm-80)
REVERT: C   73 ASN cc_start: 0.8536 (t0) cc_final: 0.8189 (t160)
REVERT: C   91 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.5814 (mp0)
REVERT: E   53 ARG cc_start: 0.8689 (tmm-80) cc_final: 0.8480 (ttt-90)
REVERT: F   93 GLN cc_start: 0.8456 (mt0) cc_final: 0.8234 (mt0)
REVERT: G   73 ASN cc_start: 0.8414 (t0) cc_final: 0.8123 (t0)
REVERT: G   91 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.3460 (tp30)
  outliers start: 16
  outliers final: 10
  residues processed: 164
  average time/residue: 2.8587
  time to fit residues: 490.9832
Evaluate side-chains
  170 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 156
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
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 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
Chi-restraints excluded: chain H residue  120 LYS
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:    0.0980
   chunk 34 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0970
   chunk 59 optimal weight:    4.9990
   chunk 80 optimal weight:    5.9990
   chunk 35 optimal weight:    7.9990
   chunk 45 optimal weight:    0.5980
   chunk 73 optimal weight:    5.9990
   chunk 55 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
D  84 ASN
E  68 GLN
F  27 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.098741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.086263 restraints weight = 18228.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 0.96
r_work: 0.3126 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12645  Z= 0.160
  Angle     :  0.577  10.986  18321  Z= 0.353
  Chirality :  0.034   0.133   2083
  Planarity :  0.004   0.031   1316
  Dihedral  : 30.385  95.273   4003
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 20.94 %
    Favored  : 76.95 %
  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:  3.39 (0.30), residues: 730
  helix:  3.05 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.15 (0.40), 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   0.010   0.001   TYR F  88 
 ARG   0.004   0.000   ARG E  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04724 (  781)
  hydrogen bonds       : angle       2.72384 ( 1948)
  covalent geometry    : bond        0.00338 (12645)
  covalent geometry    : angle       0.57750 (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
  171 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 158
  time to evaluate  : 0.895 
Fit side-chains
REVERT: A   83 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8238 (mtt90)
REVERT: A  129 ARG cc_start: 0.8250 (mmm160) cc_final: 0.7833 (tpt90)
REVERT: B   35 ARG cc_start: 0.8588 (mtp85) cc_final: 0.8337 (mtp85)
REVERT: B   93 GLN cc_start: 0.8392 (mt0) cc_final: 0.8174 (mm-40)
REVERT: C   11 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7544 (pmm-80)
REVERT: C   73 ASN cc_start: 0.8535 (t0) cc_final: 0.8160 (t160)
REVERT: C   91 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.5798 (mp0)
REVERT: G   73 ASN cc_start: 0.8397 (t0) cc_final: 0.8104 (t0)
REVERT: G   91 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.3425 (tp30)
  outliers start: 13
  outliers final: 7
  residues processed: 165
  average time/residue: 2.0415
  time to fit residues: 353.0879
Evaluate side-chains
  170 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 159
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
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 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
Chi-restraints excluded: chain H residue  120 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 80 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0770
   chunk 68 optimal weight:    0.7980
   chunk 91 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   chunk 17 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.6338

-------------------------------------------------------------------------------
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
F  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.099267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.086795 restraints weight = 18264.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 0.97
r_work: 0.3127 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12645  Z= 0.161
  Angle     :  0.567   9.522  18321  Z= 0.350
  Chirality :  0.034   0.133   2083
  Planarity :  0.004   0.034   1316
  Dihedral  : 30.373  95.158   4003
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 21.10 %
    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:  3.38 (0.30), residues: 730
  helix:  3.04 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.15 (0.40), 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   0.017   0.001   TYR F  88 
 ARG   0.004   0.000   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04686 (  781)
  hydrogen bonds       : angle       2.71145 ( 1948)
  covalent geometry    : bond        0.00340 (12645)
  covalent geometry    : angle       0.56659 (18321)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10888.86 seconds
wall clock time: 195 minutes 9.89 seconds (11709.89 seconds total)