Starting phenix.real_space_refine
on Fri Sep 11 20:39:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k41_62038/09_2026/9k41_62038.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k41_62038/09_2026/9k41_62038.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k41_62038/09_2026/9k41_62038.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k41_62038/09_2026/9k41_62038.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k41_62038/09_2026/9k41_62038.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k41_62038/09_2026/9k41_62038.cif"
  }
  resolution = 2.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.052
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      14      5.16       5
     C    6585      2.51       5
     N    2168      2.21       5
     O    2772      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11828
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 783
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 644
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 785
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 783
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 644
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 785
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "H"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2950
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2992
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2992
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.14, per 1000 atoms: 0.18
  Number of scatterers: 11828
  At special positions: 0
  Unit cell: (121.136, 75.04, 114.704, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     289     15.00
     O    2772      8.00
     N    2168      7.00
     C    6585      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 344.2 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:  1388

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 10 sheets defined
      72.3% alpha, 3.2% beta
      145 base pairs and 259 stacking pairs defined.
    Time for finding SS restraints: 1.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.559A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.677A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.644A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 25 through 31
      removed outlier: 3.546A  pdb=" N   ALA C  30 " --> pdb=" O   LYS C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 46
    Processing helix  chain 'C' and resid 55 through 82
    Processing helix  chain 'C' and resid 88 through 99
    Processing helix  chain 'C' and resid 99 through 106
    Processing helix  chain 'D' and resid 60 through 72
    Processing helix  chain 'D' and resid 78 through 107
    Processing helix  chain 'D' and resid 113 through 125
    Processing helix  chain 'D' and resid 127 through 147
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.687A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.598A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 25 through 31
    Processing helix  chain 'G' and resid 35 through 46
    Processing helix  chain 'G' and resid 55 through 82
    Processing helix  chain 'G' and resid 88 through 98
    Processing helix  chain 'G' and resid 99 through 106
    Processing helix  chain 'H' and resid 60 through 72
    Processing helix  chain 'H' and resid 78 through 107
    Processing helix  chain 'H' and resid 113 through 125
    Processing helix  chain 'H' and resid 126 through 147
      removed outlier: 3.528A  pdb=" N   ALA H 130 " --> pdb=" O   PRO H 126 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.044A  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
      removed outlier: 6.439A  pdb=" N   THR B  96 " --> pdb=" O   THR G 110 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 51 through 52
      removed outlier: 7.447A  pdb=" N   ARG C  51 " --> pdb=" O   ILE D 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 86 through 87
    Processing sheet with id=AA6, first strand: chain 'C' and resid 109 through 111
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.111A  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 51 through 52
      removed outlier: 7.241A  pdb=" N   ARG G  51 " --> pdb=" O   ILE H 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 86 through 87

    405 hydrogen bonds defined for protein.
    1206 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      348 hydrogen bonds
      696 hydrogen bond angles
      0 basepair planarities
      145 basepair parallelities
      259 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2177
        1.33 -     1.45: 4095
        1.45 -     1.57: 5758
        1.57 -     1.69: 577
        1.69 -     1.81: 26
  Bond restraints: 12633
  Sorted by residual:
  bond pdb=" O3'  DC J -26 "
       pdb=" P    DA J -25 "
    ideal  model  delta    sigma   weight residual
    1.607  1.653 -0.046 1.20e-02 6.94e+03 1.46e+01
  bond pdb=" C3'  DT I  22 "
       pdb=" C2'  DT I  22 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.19e+01
  bond pdb=" C3'  DG I  61 "
       pdb=" C2'  DG I  61 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.04e+01
  bond pdb=" C3'  DC J  64 "
       pdb=" C2'  DC J  64 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.68e+00
  bond pdb=" C3'  DT I  52 "
       pdb=" C2'  DT I  52 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.41e+00
  ... (remaining 12628 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 15921
        1.03 -     2.07: 1688
        2.07 -     3.10: 640
        3.10 -     4.13: 40
        4.13 -     5.17: 10
  Bond angle restraints: 18299
  Sorted by residual:
  angle pdb=" N3   DT I   8 "
        pdb=" C4   DT I   8 "
        pdb=" O4   DT I   8 "
      ideal   model   delta    sigma   weight residual
     119.90  122.60   -2.70 6.00e-01 2.78e+00 2.02e+01
  angle pdb=" N3   DT J  51 "
        pdb=" C4   DT J  51 "
        pdb=" O4   DT J  51 "
      ideal   model   delta    sigma   weight residual
     119.90  122.53   -2.63 6.00e-01 2.78e+00 1.92e+01
  angle pdb=" N3   DT J -42 "
        pdb=" C4   DT J -42 "
        pdb=" O4   DT J -42 "
      ideal   model   delta    sigma   weight residual
     119.90  122.52   -2.62 6.00e-01 2.78e+00 1.91e+01
  angle pdb=" N3   DT I -33 "
        pdb=" C4   DT I -33 "
        pdb=" O4   DT I -33 "
      ideal   model   delta    sigma   weight residual
     119.90  122.50   -2.60 6.00e-01 2.78e+00 1.88e+01
  angle pdb=" N3   DT I  29 "
        pdb=" C4   DT I  29 "
        pdb=" O4   DT I  29 "
      ideal   model   delta    sigma   weight residual
     119.90  122.50   -2.60 6.00e-01 2.78e+00 1.88e+01
  ... (remaining 18294 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.84: 4451
       20.84 -    41.69: 1347
       41.69 -    62.53: 1084
       62.53 -    83.38: 50
       83.38 -   104.22: 3
  Dihedral angle restraints: 6935
    sinusoidal: 4785
      harmonic: 2150
  Sorted by residual:
  dihedral pdb=" CA  PRO H 126 "
           pdb=" C   PRO H 126 "
           pdb=" N   GLY H 127 "
           pdb=" CA  GLY H 127 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.93   16.07     0      5.00e+00 4.00e-02 1.03e+01
  dihedral pdb=" CG  ARG A  49 "
           pdb=" CD  ARG A  49 "
           pdb=" NE  ARG A  49 "
           pdb=" CZ  ARG A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  132.97  -42.97     2      1.50e+01 4.44e-03 9.91e+00
  dihedral pdb=" C4'  DG J -17 "
           pdb=" C3'  DG J -17 "
           pdb=" O3'  DG J -17 "
           pdb=" P    DC J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00  -35.78 -104.22     1      3.50e+01 8.16e-04 9.76e+00
  ... (remaining 6932 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1317
       0.038 -    0.077: 564
       0.077 -    0.115: 183
       0.115 -    0.153: 22
       0.153 -    0.192: 1
  Chirality restraints: 2087
  Sorted by residual:
  chirality pdb=" CA  ASP F  24 "
            pdb=" N   ASP F  24 "
            pdb=" C   ASP F  24 "
            pdb=" CB  ASP F  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.19e-01
  chirality pdb=" P    DA I  -8 "
            pdb=" OP1  DA I  -8 "
            pdb=" OP2  DA I  -8 "
            pdb=" O5'  DA I  -8 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.48   -0.14 2.00e-01 2.50e+01 5.21e-01
  chirality pdb=" C3'  DC I -62 "
            pdb=" C4'  DC I -62 "
            pdb=" O3'  DC I -62 "
            pdb=" C2'  DC I -62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.60   -0.13 2.00e-01 2.50e+01 4.44e-01
  ... (remaining 2084 not shown)

  Planarity restraints: 1304
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H 125 "    0.027 5.00e-02 4.00e+02   4.05e-02 2.63e+00
        pdb=" N   PRO H 126 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO H 126 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO H 126 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  44 "    0.011 2.00e-02 2.50e+03   1.07e-02 2.60e+00
        pdb=" N1   DC J  44 "   -0.013 2.00e-02 2.50e+03
        pdb=" C2   DC J  44 "    0.021 2.00e-02 2.50e+03
        pdb=" O2   DC J  44 "   -0.014 2.00e-02 2.50e+03
        pdb=" N3   DC J  44 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DC J  44 "    0.008 2.00e-02 2.50e+03
        pdb=" N4   DC J  44 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5   DC J  44 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DC J  44 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 125 "   -0.025 5.00e-02 4.00e+02   3.79e-02 2.29e+00
        pdb=" N   PRO D 126 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO D 126 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 126 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1301 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1308
        2.75 -     3.29: 10382
        3.29 -     3.82: 23519
        3.82 -     4.36: 27964
        4.36 -     4.90: 39816
  Nonbonded interactions: 102989
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS D  55 "
            pdb=" OP1  DT I -46 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" NH2 ARG G  41 "
            pdb=" OE1 GLU H  58 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" O   SER G  85 "
            pdb=" OG  SER G  85 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH1 ARG A 131 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH1 ARG E 131 "
     model   vdw
     2.309 3.120
  ... (remaining 102984 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.040
  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:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     10.530
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
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      :  0.006   0.046  12633  Z= 0.515
  Angle     :  0.741   5.167  18299  Z= 0.684
  Chirality :  0.045   0.192   2087
  Planarity :  0.004   0.041   1304
  Dihedral  : 28.881 104.221   5547
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 22.99 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.93 (0.30), residues: 730
  helix:  1.71 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop :  0.08 (0.42), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  92 
 TYR   0.010   0.002   TYR B  98 
 PHE   0.006   0.001   PHE C  34 
 HIS   0.002   0.000   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00588 /  0.52 (12633)
  covalent geometry    : angle       0.74105 /  0.68 (18299)
  hydrogen bonds       : bond        0.12474 /  8.56 (  753)
  hydrogen bonds       : angle       4.65008 /  3.36 ( 1902)

*********************** 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
  152 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 144
  time to evaluate  : 0.310 
Fit side-chains
REVERT: C   81 ASP cc_start: 0.8800 (m-30) cc_final: 0.8594 (m-30)
REVERT: C   99 ASP cc_start: 0.8819 (t70) cc_final: 0.7685 (t0)
REVERT: C  121 ASN cc_start: 0.9301 (t0) cc_final: 0.8789 (t0)
REVERT: D   82 MET cc_start: 0.9307 (tpt) cc_final: 0.9096 (mmm)
REVERT: D   91 ASP cc_start: 0.9111 (t70) cc_final: 0.8801 (t0)
REVERT: G   81 ASP cc_start: 0.8985 (m-30) cc_final: 0.8775 (m-30)
REVERT: G   99 ASP cc_start: 0.8900 (t70) cc_final: 0.8635 (t0)
REVERT: G  121 ASN cc_start: 0.9264 (t0) cc_final: 0.8854 (t0)
REVERT: H   58 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8145 (mm-30)
REVERT: H   91 ASP cc_start: 0.9098 (t0) cc_final: 0.8782 (t0)
REVERT: H  128 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8131 (tm-30)
  outliers start: 8
  outliers final: 0
  residues processed: 148
  average time/residue: 0.7673
  time to fit residues: 120.4510
Evaluate side-chains
  110 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
A 108 ASN
A 113 HIS
B  25 ASN
B  27 GLN
B  75 HIS
C  33 GLN
C  82 ASN
D  56 ASN
E  68 GLN
E 108 ASN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  75 HIS
G  33 GLN
G  77 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.053903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.037492 restraints weight = 52413.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.2884 rms_B_bonded: 1.93
r_work: 0.2723 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8818
moved from start:          0.1216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12633  Z= 0.180
  Angle     :  0.670   8.530  18299  Z= 0.390
  Chirality :  0.044   0.223   2087
  Planarity :  0.004   0.040   1304
  Dihedral  : 31.345 112.465   4071
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 23.31 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.68 (0.31), residues: 730
  helix:  2.36 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.09 (0.44), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  23 
 TYR   0.011   0.002   TYR H  63 
 PHE   0.006   0.001   PHE D 144 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.18 (12633)
  covalent geometry    : angle       0.67022 /  0.39 (18299)
  hydrogen bonds       : bond        0.05655 /  3.82 (  753)
  hydrogen bonds       : angle       3.08434 /  2.29 ( 1902)

*********************** 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
  131 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8736 (pm20) cc_final: 0.8532 (pm20)
REVERT: C   81 ASP cc_start: 0.9066 (m-30) cc_final: 0.8816 (m-30)
REVERT: C   99 ASP cc_start: 0.8724 (t70) cc_final: 0.7735 (t0)
REVERT: C  101 GLU cc_start: 0.8324 (pm20) cc_final: 0.7886 (pm20)
REVERT: C  121 ASN cc_start: 0.9311 (OUTLIER) cc_final: 0.8719 (t0)
REVERT: D   82 MET cc_start: 0.9365 (tpt) cc_final: 0.9110 (mmm)
REVERT: D   91 ASP cc_start: 0.9323 (t70) cc_final: 0.8966 (t0)
REVERT: D   98 GLN cc_start: 0.9355 (mm-40) cc_final: 0.9104 (mm-40)
REVERT: D  128 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8405 (tp30)
REVERT: G   81 ASP cc_start: 0.9156 (m-30) cc_final: 0.8877 (m-30)
REVERT: G   99 ASP cc_start: 0.9178 (t70) cc_final: 0.8662 (t0)
REVERT: G  121 ASN cc_start: 0.9255 (OUTLIER) cc_final: 0.8760 (t0)
REVERT: H   58 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8217 (mm-30)
REVERT: H   91 ASP cc_start: 0.9279 (t0) cc_final: 0.8911 (t0)
REVERT: H   94 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8442 (tm-30)
REVERT: H  128 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8380 (tm-30)
  outliers start: 13
  outliers final: 4
  residues processed: 127
  average time/residue: 0.7597
  time to fit residues: 102.1181
Evaluate side-chains
  117 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain G residue  122 SER
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 88 optimal weight:   30.0000
   chunk 95 optimal weight:   20.0000
   chunk 48 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 17 optimal weight:    9.9990
   chunk 44 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    1.5184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 113 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.053831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.037481 restraints weight = 52962.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.2885 rms_B_bonded: 1.92
r_work: 0.2725 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8814
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12633  Z= 0.149
  Angle     :  0.615   7.345  18299  Z= 0.366
  Chirality :  0.042   0.217   2087
  Planarity :  0.004   0.039   1304
  Dihedral  : 31.438 113.490   4071
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 22.19 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.94 (0.31), residues: 730
  helix:  2.53 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.02 (0.45), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  23 
 TYR   0.011   0.001   TYR H  63 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.15 (12633)
  covalent geometry    : angle       0.61535 /  0.37 (18299)
  hydrogen bonds       : bond        0.04754 /  3.17 (  753)
  hydrogen bonds       : angle       2.84240 /  2.11 ( 1902)

*********************** 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
  131 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8803 (pm20) cc_final: 0.8519 (pm20)
REVERT: B   50 ILE cc_start: 0.9461 (mm) cc_final: 0.9201 (mp)
REVERT: C   81 ASP cc_start: 0.9095 (m-30) cc_final: 0.8854 (m-30)
REVERT: C   83 LYS cc_start: 0.9471 (tppp) cc_final: 0.9258 (tptp)
REVERT: C   99 ASP cc_start: 0.8610 (t70) cc_final: 0.7779 (t0)
REVERT: C  101 GLU cc_start: 0.8298 (pm20) cc_final: 0.7716 (pm20)
REVERT: C  121 ASN cc_start: 0.9302 (OUTLIER) cc_final: 0.8688 (t0)
REVERT: D   82 MET cc_start: 0.9414 (tpt) cc_final: 0.9118 (mmm)
REVERT: D   91 ASP cc_start: 0.9337 (t70) cc_final: 0.8964 (t0)
REVERT: D   94 GLU cc_start: 0.9234 (tp30) cc_final: 0.8927 (tp30)
REVERT: D   98 GLN cc_start: 0.9405 (mm-40) cc_final: 0.9183 (mm-40)
REVERT: D  128 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8343 (tp30)
REVERT: F   92 ARG cc_start: 0.9480 (OUTLIER) cc_final: 0.9086 (mtp-110)
REVERT: G   81 ASP cc_start: 0.9123 (m-30) cc_final: 0.8898 (m-30)
REVERT: G   99 ASP cc_start: 0.9143 (t70) cc_final: 0.8355 (t0)
REVERT: G  121 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8689 (t0)
REVERT: H   58 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8226 (mm-30)
REVERT: H   91 ASP cc_start: 0.9280 (t0) cc_final: 0.8910 (t0)
REVERT: H   94 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8509 (tm-30)
REVERT: H  128 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8368 (tm-30)
  outliers start: 11
  outliers final: 3
  residues processed: 129
  average time/residue: 0.7688
  time to fit residues: 104.9736
Evaluate side-chains
  117 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 95 optimal weight:   20.0000
   chunk 20 optimal weight:    0.8980
   chunk 85 optimal weight:   40.0000
   chunk 35 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 97 optimal weight:   20.0000
   chunk 92 optimal weight:   10.0000
   chunk 81 optimal weight:   20.0000
   chunk 90 optimal weight:   20.0000
   chunk 23 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    1.7584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  82 ASN
H 107 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.053068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.037067 restraints weight = 53222.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.2874 rms_B_bonded: 1.90
r_work: 0.2713 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8831
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12633  Z= 0.155
  Angle     :  0.623   7.991  18299  Z= 0.364
  Chirality :  0.042   0.214   2087
  Planarity :  0.004   0.048   1304
  Dihedral  : 31.530 113.955   4071
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 22.51 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.15 (0.31), residues: 730
  helix:  2.68 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.09 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 105 
 TYR   0.010   0.001   TYR H  63 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.15 (12633)
  covalent geometry    : angle       0.62303 /  0.36 (18299)
  hydrogen bonds       : bond        0.04810 /  3.24 (  753)
  hydrogen bonds       : angle       2.75606 /  2.05 ( 1902)

*********************** 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
  129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8886 (pm20) cc_final: 0.8541 (pm20)
REVERT: C   81 ASP cc_start: 0.9113 (m-30) cc_final: 0.8869 (m-30)
REVERT: C   99 ASP cc_start: 0.8630 (t70) cc_final: 0.7564 (t70)
REVERT: C  101 GLU cc_start: 0.8344 (pm20) cc_final: 0.7810 (pm20)
REVERT: C  121 ASN cc_start: 0.9273 (OUTLIER) cc_final: 0.8688 (t0)
REVERT: D   82 MET cc_start: 0.9463 (tpt) cc_final: 0.9140 (mmm)
REVERT: D   91 ASP cc_start: 0.9357 (t70) cc_final: 0.8979 (t0)
REVERT: D   94 GLU cc_start: 0.9223 (tp30) cc_final: 0.8889 (tp30)
REVERT: D   98 GLN cc_start: 0.9380 (mm-40) cc_final: 0.9159 (mm-40)
REVERT: D  128 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8343 (tp30)
REVERT: F   92 ARG cc_start: 0.9477 (OUTLIER) cc_final: 0.9125 (mtp-110)
REVERT: G   81 ASP cc_start: 0.9135 (m-30) cc_final: 0.8925 (m-30)
REVERT: G   99 ASP cc_start: 0.9021 (t70) cc_final: 0.8433 (t0)
REVERT: G  104 LYS cc_start: 0.9571 (ttmt) cc_final: 0.9225 (ttmm)
REVERT: G  121 ASN cc_start: 0.9214 (OUTLIER) cc_final: 0.8702 (t0)
REVERT: H   58 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8207 (mm-30)
REVERT: H   91 ASP cc_start: 0.9294 (t0) cc_final: 0.8911 (t0)
REVERT: H   94 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8488 (tm-30)
REVERT: H  128 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8329 (tm-30)
  outliers start: 9
  outliers final: 4
  residues processed: 126
  average time/residue: 0.8256
  time to fit residues: 109.9451
Evaluate side-chains
  120 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain G residue  122 SER
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 62 optimal weight:    8.9990
   chunk 25 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 75 optimal weight:   20.0000
   chunk 19 optimal weight:    7.9990
   chunk 64 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 73 optimal weight:   40.0000
   chunk 86 optimal weight:   30.0000
   chunk 33 optimal weight:    0.9980
   overall best weight:    2.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
G  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.051996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.035612 restraints weight = 53319.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.2831 rms_B_bonded: 1.92
r_work: 0.2671 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8868
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12633  Z= 0.208
  Angle     :  0.665   9.156  18299  Z= 0.377
  Chirality :  0.043   0.221   2087
  Planarity :  0.004   0.042   1304
  Dihedral  : 31.731 113.290   4071
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 22.51 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.16 (0.31), residues: 730
  helix:  2.70 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.04 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.026   0.001   ARG B  23 
 TYR   0.010   0.001   TYR B  88 
 PHE   0.008   0.001   PHE C  34 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00420 /  0.21 (12633)
  covalent geometry    : angle       0.66481 /  0.38 (18299)
  hydrogen bonds       : bond        0.05548 /  3.76 (  753)
  hydrogen bonds       : angle       2.86101 /  2.13 ( 1902)

*********************** 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
  124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8935 (pm20) cc_final: 0.8636 (pm20)
REVERT: C   81 ASP cc_start: 0.9134 (m-30) cc_final: 0.8921 (m-30)
REVERT: C   99 ASP cc_start: 0.8733 (t70) cc_final: 0.7782 (t0)
REVERT: C  101 GLU cc_start: 0.8304 (pm20) cc_final: 0.7795 (pm20)
REVERT: C  121 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.8706 (t0)
REVERT: D   82 MET cc_start: 0.9494 (tpt) cc_final: 0.9148 (mmm)
REVERT: D   91 ASP cc_start: 0.9381 (t70) cc_final: 0.9009 (t0)
REVERT: D   94 GLU cc_start: 0.9251 (tp30) cc_final: 0.8841 (tp30)
REVERT: D   98 GLN cc_start: 0.9408 (mm-40) cc_final: 0.9151 (mm-40)
REVERT: D  128 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8456 (tp30)
REVERT: E   79 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8958 (tttp)
REVERT: F   53 GLU cc_start: 0.9146 (tp30) cc_final: 0.8944 (mm-30)
REVERT: F   92 ARG cc_start: 0.9476 (OUTLIER) cc_final: 0.9152 (mtp-110)
REVERT: G   81 ASP cc_start: 0.9166 (m-30) cc_final: 0.8963 (m-30)
REVERT: G   99 ASP cc_start: 0.9089 (t70) cc_final: 0.8542 (t0)
REVERT: G  100 GLU cc_start: 0.8660 (tp30) cc_final: 0.8375 (tp30)
REVERT: G  104 LYS cc_start: 0.9585 (ttmt) cc_final: 0.9316 (ttmm)
REVERT: G  121 ASN cc_start: 0.9228 (OUTLIER) cc_final: 0.8705 (t0)
REVERT: H   58 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8072 (mm-30)
REVERT: H   91 ASP cc_start: 0.9323 (t0) cc_final: 0.8968 (t0)
REVERT: H   94 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8551 (tm-30)
REVERT: H  128 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8375 (tm-30)
  outliers start: 11
  outliers final: 5
  residues processed: 121
  average time/residue: 0.7855
  time to fit residues: 100.5797
Evaluate side-chains
  120 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   79 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain G residue  122 SER
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 17 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9990
   chunk 92 optimal weight:   10.0000
   chunk 76 optimal weight:   20.0000
   chunk 37 optimal weight:    1.9990
   chunk 90 optimal weight:   20.0000
   chunk 68 optimal weight:    0.4980
   chunk 16 optimal weight:    5.9990
   overall best weight:    2.0988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.051999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.036015 restraints weight = 53201.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 1.90
r_work: 0.2681 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
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      :  0.003   0.033  12633  Z= 0.163
  Angle     :  0.639  10.408  18299  Z= 0.366
  Chirality :  0.042   0.220   2087
  Planarity :  0.004   0.039   1304
  Dihedral  : 31.745 115.469   4071
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 22.99 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.26 (0.31), residues: 730
  helix:  2.77 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.07 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 105 
 TYR   0.008   0.001   TYR H  63 
 PHE   0.006   0.001   PHE E  67 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.16 (12633)
  covalent geometry    : angle       0.63946 /  0.37 (18299)
  hydrogen bonds       : bond        0.04579 /  3.06 (  753)
  hydrogen bonds       : angle       2.72002 /  2.02 ( 1902)

*********************** 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
  129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8960 (pm20) cc_final: 0.8653 (pm20)
REVERT: A   80 THR cc_start: 0.9614 (OUTLIER) cc_final: 0.9344 (m)
REVERT: C   28 MET cc_start: 0.9098 (ptt) cc_final: 0.8847 (ppp)
REVERT: C   81 ASP cc_start: 0.9117 (m-30) cc_final: 0.8906 (m-30)
REVERT: C   99 ASP cc_start: 0.8749 (t70) cc_final: 0.7868 (t70)
REVERT: C  101 GLU cc_start: 0.8297 (pm20) cc_final: 0.7768 (pm20)
REVERT: C  121 ASN cc_start: 0.9248 (OUTLIER) cc_final: 0.8711 (t0)
REVERT: D   82 MET cc_start: 0.9496 (tpt) cc_final: 0.9107 (mmm)
REVERT: D   91 ASP cc_start: 0.9360 (t70) cc_final: 0.8988 (t0)
REVERT: D   94 GLU cc_start: 0.9223 (tp30) cc_final: 0.8593 (tm-30)
REVERT: D   98 GLN cc_start: 0.9395 (mm-40) cc_final: 0.9086 (mm-40)
REVERT: D  106 TYR cc_start: 0.8895 (m-10) cc_final: 0.8425 (m-80)
REVERT: D  128 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8424 (tp30)
REVERT: F   53 GLU cc_start: 0.9144 (tp30) cc_final: 0.8930 (mm-30)
REVERT: F   92 ARG cc_start: 0.9470 (OUTLIER) cc_final: 0.9150 (mtp-110)
REVERT: G   99 ASP cc_start: 0.9108 (t70) cc_final: 0.8575 (t0)
REVERT: G  100 GLU cc_start: 0.8638 (tp30) cc_final: 0.8122 (tm-30)
REVERT: G  104 LYS cc_start: 0.9544 (ttmt) cc_final: 0.9181 (ttmm)
REVERT: G  121 ASN cc_start: 0.9232 (OUTLIER) cc_final: 0.8725 (t0)
REVERT: H   58 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8122 (mm-30)
REVERT: H   91 ASP cc_start: 0.9309 (t0) cc_final: 0.8936 (t0)
REVERT: H   94 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8523 (tm-30)
REVERT: H  128 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8372 (tm-30)
  outliers start: 12
  outliers final: 4
  residues processed: 126
  average time/residue: 0.7153
  time to fit residues: 95.7749
Evaluate side-chains
  122 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 89 optimal weight:   20.0000
   chunk 21 optimal weight:    2.9990
   chunk 88 optimal weight:   30.0000
   chunk 84 optimal weight:   20.0000
   chunk 3 optimal weight:    0.0870
   chunk 91 optimal weight:   20.0000
   chunk 2 optimal weight:    3.9990
   chunk 80 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9980
   overall best weight:    2.0164

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  82 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.051697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.035835 restraints weight = 53075.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 1.90
r_work: 0.2677 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8870
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12633  Z= 0.162
  Angle     :  0.645   9.707  18299  Z= 0.365
  Chirality :  0.042   0.219   2087
  Planarity :  0.004   0.037   1304
  Dihedral  : 31.748 116.649   4071
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 22.67 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.30 (0.31), residues: 730
  helix:  2.80 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.08 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 105 
 TYR   0.012   0.001   TYR F  88 
 PHE   0.006   0.001   PHE E  67 
 HIS   0.002   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.16 (12633)
  covalent geometry    : angle       0.64542 /  0.37 (18299)
  hydrogen bonds       : bond        0.04717 /  3.17 (  753)
  hydrogen bonds       : angle       2.68326 /  2.00 ( 1902)

*********************** 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
  127 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8955 (pm20) cc_final: 0.8647 (pm20)
REVERT: A   80 THR cc_start: 0.9565 (OUTLIER) cc_final: 0.9306 (m)
REVERT: C   28 MET cc_start: 0.9074 (ptt) cc_final: 0.8848 (ppp)
REVERT: C   81 ASP cc_start: 0.9118 (m-30) cc_final: 0.8882 (m-30)
REVERT: C   82 ASN cc_start: 0.9418 (t0) cc_final: 0.9065 (t0)
REVERT: C   99 ASP cc_start: 0.8714 (t70) cc_final: 0.7835 (t70)
REVERT: C  101 GLU cc_start: 0.8300 (pm20) cc_final: 0.7592 (pm20)
REVERT: C  121 ASN cc_start: 0.9237 (OUTLIER) cc_final: 0.8699 (t0)
REVERT: D   82 MET cc_start: 0.9535 (tpt) cc_final: 0.9182 (mmm)
REVERT: D   91 ASP cc_start: 0.9356 (t70) cc_final: 0.8972 (t0)
REVERT: D   94 GLU cc_start: 0.9230 (tp30) cc_final: 0.8610 (tm-30)
REVERT: D   98 GLN cc_start: 0.9412 (mm-40) cc_final: 0.9090 (mm-40)
REVERT: D  128 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8181 (tm-30)
REVERT: F   92 ARG cc_start: 0.9464 (OUTLIER) cc_final: 0.9076 (mtp-110)
REVERT: G   99 ASP cc_start: 0.9086 (t70) cc_final: 0.8492 (t0)
REVERT: G  100 GLU cc_start: 0.8675 (tp30) cc_final: 0.8184 (tm-30)
REVERT: G  104 LYS cc_start: 0.9551 (ttmt) cc_final: 0.9155 (ttmm)
REVERT: G  121 ASN cc_start: 0.9211 (OUTLIER) cc_final: 0.8708 (t0)
REVERT: H   58 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8105 (mm-30)
REVERT: H   91 ASP cc_start: 0.9318 (t0) cc_final: 0.8948 (t0)
REVERT: H   94 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8569 (tm-30)
REVERT: H  128 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8363 (tm-30)
  outliers start: 12
  outliers final: 4
  residues processed: 124
  average time/residue: 0.7496
  time to fit residues: 98.4541
Evaluate side-chains
  121 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 99 optimal weight:   40.0000
   chunk 16 optimal weight:    0.8980
   chunk 75 optimal weight:   20.0000
   chunk 64 optimal weight:    0.9990
   chunk 70 optimal weight:    0.3980
   chunk 73 optimal weight:   40.0000
   chunk 86 optimal weight:   30.0000
   chunk 40 optimal weight:    0.3980
   chunk 72 optimal weight:   20.0000
   overall best weight:    1.1384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.052049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.036210 restraints weight = 53025.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 1.92
r_work: 0.2691 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8863
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  12633  Z= 0.132
  Angle     :  0.631  11.868  18299  Z= 0.361
  Chirality :  0.041   0.218   2087
  Planarity :  0.004   0.034   1304
  Dihedral  : 31.678 117.950   4071
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 23.15 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.33 (0.31), residues: 730
  helix:  2.82 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.11 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 105 
 TYR   0.011   0.001   TYR F  88 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.002   0.001   HIS D  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.13 (12633)
  covalent geometry    : angle       0.63143 /  0.36 (18299)
  hydrogen bonds       : bond        0.04090 /  2.73 (  753)
  hydrogen bonds       : angle       2.61541 /  1.94 ( 1902)

*********************** 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
  129 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8994 (pm20) cc_final: 0.8674 (pm20)
REVERT: A   80 THR cc_start: 0.9540 (OUTLIER) cc_final: 0.9282 (m)
REVERT: A  120 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8756 (mtt)
REVERT: C   28 MET cc_start: 0.9090 (ptt) cc_final: 0.8873 (ppp)
REVERT: C   81 ASP cc_start: 0.9111 (m-30) cc_final: 0.8888 (m-30)
REVERT: C   99 ASP cc_start: 0.8710 (t70) cc_final: 0.7833 (t70)
REVERT: C  101 GLU cc_start: 0.8250 (pm20) cc_final: 0.7799 (pm20)
REVERT: C  121 ASN cc_start: 0.9223 (OUTLIER) cc_final: 0.8699 (t0)
REVERT: D   82 MET cc_start: 0.9539 (tpt) cc_final: 0.9229 (mmm)
REVERT: D   91 ASP cc_start: 0.9350 (t0) cc_final: 0.8978 (t0)
REVERT: D   94 GLU cc_start: 0.9218 (tp30) cc_final: 0.8606 (tm-30)
REVERT: D   98 GLN cc_start: 0.9396 (mm-40) cc_final: 0.9066 (mm-40)
REVERT: D  128 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8161 (tm-30)
REVERT: E   80 THR cc_start: 0.9559 (OUTLIER) cc_final: 0.9270 (m)
REVERT: F   92 ARG cc_start: 0.9439 (OUTLIER) cc_final: 0.9193 (mtp-110)
REVERT: G   28 MET cc_start: 0.9179 (ttp) cc_final: 0.8852 (ptt)
REVERT: G   99 ASP cc_start: 0.9161 (t70) cc_final: 0.8586 (t0)
REVERT: G  100 GLU cc_start: 0.8670 (tp30) cc_final: 0.8209 (tm-30)
REVERT: G  104 LYS cc_start: 0.9544 (ttmt) cc_final: 0.9152 (ttmm)
REVERT: G  121 ASN cc_start: 0.9203 (OUTLIER) cc_final: 0.8710 (t0)
REVERT: H   58 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8118 (mm-30)
REVERT: H   91 ASP cc_start: 0.9285 (t0) cc_final: 0.8900 (t0)
REVERT: H   94 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8606 (tm-30)
REVERT: H  128 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8348 (tm-30)
  outliers start: 12
  outliers final: 4
  residues processed: 125
  average time/residue: 0.7655
  time to fit residues: 101.3981
Evaluate side-chains
  125 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 22 optimal weight:    9.9990
   chunk 89 optimal weight:   20.0000
   chunk 7 optimal weight:    1.9990
   chunk 91 optimal weight:   20.0000
   chunk 74 optimal weight:   30.0000
   chunk 9 optimal weight:    1.9990
   chunk 88 optimal weight:   30.0000
   chunk 35 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN
A  76 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.052120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.036314 restraints weight = 52639.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 1.90
r_work: 0.2694 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8858
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12633  Z= 0.137
  Angle     :  0.637  12.239  18299  Z= 0.363
  Chirality :  0.041   0.216   2087
  Planarity :  0.004   0.036   1304
  Dihedral  : 31.622 118.421   4071
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 23.63 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.38 (0.31), residues: 730
  helix:  2.86 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.12 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 105 
 TYR   0.008   0.001   TYR H  63 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.002   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.14 (12633)
  covalent geometry    : angle       0.63704 /  0.36 (18299)
  hydrogen bonds       : bond        0.04213 /  2.81 (  753)
  hydrogen bonds       : angle       2.60341 /  1.94 ( 1902)

*********************** 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
  127 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8979 (pm20) cc_final: 0.8665 (pm20)
REVERT: A   80 THR cc_start: 0.9532 (OUTLIER) cc_final: 0.9284 (m)
REVERT: C   28 MET cc_start: 0.9095 (ptt) cc_final: 0.8878 (ppp)
REVERT: C   81 ASP cc_start: 0.9114 (m-30) cc_final: 0.8879 (m-30)
REVERT: C   99 ASP cc_start: 0.8708 (t70) cc_final: 0.7853 (t70)
REVERT: C  101 GLU cc_start: 0.8203 (pm20) cc_final: 0.7651 (pm20)
REVERT: C  121 ASN cc_start: 0.9205 (OUTLIER) cc_final: 0.8679 (t0)
REVERT: D   82 MET cc_start: 0.9530 (tpt) cc_final: 0.9295 (mmm)
REVERT: D   91 ASP cc_start: 0.9362 (t0) cc_final: 0.8987 (t0)
REVERT: D   94 GLU cc_start: 0.9222 (tp30) cc_final: 0.8646 (tm-30)
REVERT: D  106 TYR cc_start: 0.8866 (m-10) cc_final: 0.8350 (m-80)
REVERT: D  128 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8155 (tm-30)
REVERT: E   80 THR cc_start: 0.9542 (OUTLIER) cc_final: 0.9261 (m)
REVERT: F   92 ARG cc_start: 0.9442 (OUTLIER) cc_final: 0.9221 (mtp-110)
REVERT: G   28 MET cc_start: 0.9192 (ttp) cc_final: 0.8877 (ptt)
REVERT: G   99 ASP cc_start: 0.9181 (t70) cc_final: 0.8670 (t0)
REVERT: G  100 GLU cc_start: 0.8672 (tp30) cc_final: 0.8176 (tm-30)
REVERT: G  104 LYS cc_start: 0.9558 (ttmt) cc_final: 0.9135 (ttmm)
REVERT: G  121 ASN cc_start: 0.9185 (OUTLIER) cc_final: 0.8708 (t0)
REVERT: H   58 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8114 (mm-30)
REVERT: H   91 ASP cc_start: 0.9282 (t0) cc_final: 0.8904 (t0)
REVERT: H   94 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8592 (tm-30)
REVERT: H  128 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8335 (tm-30)
  outliers start: 12
  outliers final: 5
  residues processed: 124
  average time/residue: 0.7607
  time to fit residues: 99.9811
Evaluate side-chains
  124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   chunk 48 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 86 optimal weight:   30.0000
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
C  82 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.052295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.036534 restraints weight = 52961.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 1.92
r_work: 0.2704 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8855
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051  12633  Z= 0.130
  Angle     :  0.635  12.636  18299  Z= 0.363
  Chirality :  0.041   0.216   2087
  Planarity :  0.004   0.034   1304
  Dihedral  : 31.581 119.199   4071
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 23.31 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.39 (0.31), residues: 730
  helix:  2.87 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.13 (0.46), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 105 
 TYR   0.011   0.001   TYR F  88 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.13 (12633)
  covalent geometry    : angle       0.63463 /  0.36 (18299)
  hydrogen bonds       : bond        0.03978 /  2.65 (  753)
  hydrogen bonds       : angle       2.57772 /  1.92 ( 1902)

********************** 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
  130 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8994 (pm20) cc_final: 0.8673 (pm20)
REVERT: A   80 THR cc_start: 0.9516 (OUTLIER) cc_final: 0.9280 (m)
REVERT: A  120 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8746 (mtt)
REVERT: C   28 MET cc_start: 0.9082 (ptt) cc_final: 0.8870 (ppp)
REVERT: C   81 ASP cc_start: 0.9120 (m-30) cc_final: 0.8892 (m-30)
REVERT: C   99 ASP cc_start: 0.8691 (t70) cc_final: 0.7818 (t70)
REVERT: C  101 GLU cc_start: 0.8189 (pm20) cc_final: 0.7755 (pm20)
REVERT: C  121 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8670 (t0)
REVERT: D   82 MET cc_start: 0.9535 (tpt) cc_final: 0.9295 (mmm)
REVERT: D   91 ASP cc_start: 0.9359 (t0) cc_final: 0.8983 (t0)
REVERT: D   94 GLU cc_start: 0.9208 (tp30) cc_final: 0.8618 (tm-30)
REVERT: D  106 TYR cc_start: 0.8868 (m-10) cc_final: 0.8346 (m-80)
REVERT: D  128 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8121 (tm-30)
REVERT: E   80 THR cc_start: 0.9537 (OUTLIER) cc_final: 0.9263 (m)
REVERT: F   92 ARG cc_start: 0.9420 (OUTLIER) cc_final: 0.9170 (mtp-110)
REVERT: G   28 MET cc_start: 0.9177 (ttp) cc_final: 0.8867 (ptt)
REVERT: G   99 ASP cc_start: 0.9207 (t70) cc_final: 0.8888 (t70)
REVERT: G  100 GLU cc_start: 0.8678 (tp30) cc_final: 0.8132 (tm-30)
REVERT: G  104 LYS cc_start: 0.9529 (ttmt) cc_final: 0.9100 (ttmm)
REVERT: G  121 ASN cc_start: 0.9195 (OUTLIER) cc_final: 0.8705 (t0)
REVERT: H   58 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8112 (mm-30)
REVERT: H   91 ASP cc_start: 0.9275 (t0) cc_final: 0.8867 (t0)
REVERT: H   94 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8597 (tm-30)
REVERT: H  128 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8364 (tm-30)
  outliers start: 13
  outliers final: 5
  residues processed: 126
  average time/residue: 0.7439
  time to fit residues: 99.1517
Evaluate side-chains
  125 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 LYS
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain C residue  121 ASN
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  121 ASN
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   chunk 90 optimal weight:   20.0000
   chunk 48 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 83 optimal weight:   20.0000
   chunk 98 optimal weight:   20.0000
   overall best weight:    0.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.052614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.036839 restraints weight = 52771.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 1.93
r_work: 0.2711 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  12633  Z= 0.130
  Angle     :  0.634  12.616  18299  Z= 0.361
  Chirality :  0.041   0.214   2087
  Planarity :  0.004   0.041   1304
  Dihedral  : 31.487 119.953   4071
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 24.12 %
    Favored  : 74.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.46 (0.31), residues: 730
  helix:  2.91 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.15 (0.47), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  80 
 TYR   0.009   0.001   TYR F  88 
 PHE   0.007   0.001   PHE E  67 
 HIS   0.002   0.001   HIS D  72 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.13 (12633)
  covalent geometry    : angle       0.63442 /  0.36 (18299)
  hydrogen bonds       : bond        0.03997 /  2.65 (  753)
  hydrogen bonds       : angle       2.53925 /  1.89 ( 1902)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3464.21 seconds
wall clock time: 59 minutes 38.33 seconds (3578.33 seconds total)