Starting phenix.real_space_refine
on Wed Mar  4 08:34:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y00_33536/03_2026/7y00_33536.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y00_33536/03_2026/7y00_33536.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y00_33536/03_2026/7y00_33536.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y00_33536/03_2026/7y00_33536.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y00_33536/03_2026/7y00_33536.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y00_33536/03_2026/7y00_33536.map"
  }
  resolution = 3.96
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     310      5.49       5
     S      14      5.16       5
     C    6823      2.51       5
     N    2339      2.21       5
     O    2925      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12411
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 844
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 810
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 746
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 3166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 3166
          Classifications: {'DNA': 155}
          Link IDs: {'rna3p': 154}
    Chain: "J"
      Number of atoms: 3189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 3189
          Classifications: {'DNA': 155}
          Link IDs: {'rna3p': 154}
  Time building chain proxies: 2.52, per 1000 atoms: 0.20
  Number of scatterers: 12411
  At special positions: 0
  Unit cell: (116.6, 147.34, 113.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     310     15.00
     O    2925      8.00
     N    2339      7.00
     C    6823      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: 0.92
  Conformation dependent library (CDL) restraints added in 347.6 milliseconds
  

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1420

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      73.5% alpha, 3.1% beta
      153 base pairs and 247 stacking pairs defined.
    Time for finding SS restraints: 1.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 4.096A  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 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.292A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.117A  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 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.995A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 121
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.537A  pdb=" N   SER E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.553A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.880A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    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: 4.268A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
      removed outlier: 3.523A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 100 through 122
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.999A  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: 7.082A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (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
      removed outlier: 3.757A  pdb=" N   ILE C  78 " --> pdb=" O   GLY D  50 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
      removed outlier: 3.501A  pdb=" N   TYR F  98 " --> pdb=" O   THR C 101 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.761A  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: 7.342A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (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
      removed outlier: 3.547A  pdb=" N   ILE G  78 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    415 hydrogen bonds defined for protein.
    1218 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      395 hydrogen bonds
      786 hydrogen bond angles
      0 basepair planarities
      153 basepair parallelities
      247 stacking parallelities
  Total time for adding SS restraints: 1.81

  Time building geometry restraints manager: 1.29 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: 2627
        1.34 -     1.46: 4279
        1.46 -     1.57: 5716
        1.57 -     1.69: 618
        1.69 -     1.81: 24
  Bond restraints: 13264
  Sorted by residual:
  bond pdb=" C1'  DG J  31 "
       pdb=" N9   DG J  31 "
    ideal  model  delta    sigma   weight residual
    1.460  1.391  0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" N   ILE C  87 "
       pdb=" CA  ILE C  87 "
    ideal  model  delta    sigma   weight residual
    1.460  1.492 -0.032 1.19e-02 7.06e+03 7.08e+00
  bond pdb=" N   ILE H  66 "
       pdb=" CA  ILE H  66 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.031 1.17e-02 7.31e+03 7.02e+00
  bond pdb=" N   ILE G  87 "
       pdb=" CA  ILE G  87 "
    ideal  model  delta    sigma   weight residual
    1.460  1.491 -0.032 1.21e-02 6.83e+03 6.79e+00
  bond pdb=" N   ILE D  66 "
       pdb=" CA  ILE D  66 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.029 1.17e-02 7.31e+03 6.31e+00
  ... (remaining 13259 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 18571
        1.73 -     3.46: 609
        3.46 -     5.19: 40
        5.19 -     6.92: 15
        6.92 -     8.65: 3
  Bond angle restraints: 19238
  Sorted by residual:
  angle pdb=" N   GLN E  76 "
        pdb=" CA  GLN E  76 "
        pdb=" CB  GLN E  76 "
      ideal   model   delta    sigma   weight residual
     110.32  117.12   -6.80 1.70e+00 3.46e-01 1.60e+01
  angle pdb=" C   ALA E  75 "
        pdb=" N   GLN E  76 "
        pdb=" CA  GLN E  76 "
      ideal   model   delta    sigma   weight residual
     120.60  115.14    5.46 1.60e+00 3.91e-01 1.16e+01
  angle pdb=" N   ILE D  66 "
        pdb=" CA  ILE D  66 "
        pdb=" C   ILE D  66 "
      ideal   model   delta    sigma   weight residual
     110.42  107.17    3.25 9.60e-01 1.09e+00 1.14e+01
  angle pdb=" N   ILE H  66 "
        pdb=" CA  ILE H  66 "
        pdb=" C   ILE H  66 "
      ideal   model   delta    sigma   weight residual
     110.42  107.39    3.03 9.60e-01 1.09e+00 9.97e+00
  angle pdb=" C   GLU G  56 "
        pdb=" CA  GLU G  56 "
        pdb=" CB  GLU G  56 "
      ideal   model   delta    sigma   weight residual
     110.88  105.92    4.96 1.57e+00 4.06e-01 9.96e+00
  ... (remaining 19233 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 4655
       17.78 -    35.56: 1125
       35.56 -    53.34: 1042
       53.34 -    71.13: 324
       71.13 -    88.91: 19
  Dihedral angle restraints: 7165
    sinusoidal: 4961
      harmonic: 2204
  Sorted by residual:
  dihedral pdb=" CA  PRO D 100 "
           pdb=" C   PRO D 100 "
           pdb=" N   GLY D 101 "
           pdb=" CA  GLY D 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.74  -16.26     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CA  ILE G  87 "
           pdb=" CB  ILE G  87 "
           pdb=" CG1 ILE G  87 "
           pdb=" CD1 ILE G  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.74   57.26     3      1.50e+01 4.44e-03 9.43e+00
  dihedral pdb=" CG  ARG E 128 "
           pdb=" CD  ARG E 128 "
           pdb=" NE  ARG E 128 "
           pdb=" CZ  ARG E 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -138.72  -41.28     2      1.50e+01 4.44e-03 9.29e+00
  ... (remaining 7162 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1839
       0.046 -    0.091: 267
       0.091 -    0.137: 65
       0.137 -    0.182: 8
       0.182 -    0.228: 5
  Chirality restraints: 2184
  Sorted by residual:
  chirality pdb=" CA  GLU C  61 "
            pdb=" N   GLU C  61 "
            pdb=" C   GLU C  61 "
            pdb=" CB  GLU C  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CB  THR D 112 "
            pdb=" CA  THR D 112 "
            pdb=" OG1 THR D 112 "
            pdb=" CG2 THR D 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 8.77e-01
  chirality pdb=" CB  VAL G  54 "
            pdb=" CA  VAL G  54 "
            pdb=" CG1 VAL G  54 "
            pdb=" CG2 VAL G  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 8.69e-01
  ... (remaining 2181 not shown)

  Planarity restraints: 1361
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA G  52 "   -0.022 2.00e-02 2.50e+03   4.45e-02 1.98e+01
        pdb=" C   ALA G  52 "    0.077 2.00e-02 2.50e+03
        pdb=" O   ALA G  52 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   ALA G  53 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS F  59 "   -0.015 2.00e-02 2.50e+03   3.05e-02 9.30e+00
        pdb=" C   LYS F  59 "    0.053 2.00e-02 2.50e+03
        pdb=" O   LYS F  59 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   VAL F  60 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER E  87 "    0.008 2.00e-02 2.50e+03   1.64e-02 2.70e+00
        pdb=" C   SER E  87 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   SER E  87 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ALA E  88 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1358 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.35: 27
        2.35 -     2.99: 5762
        2.99 -     3.63: 21890
        3.63 -     4.26: 33094
        4.26 -     4.90: 47127
  Nonbonded interactions: 107900
  Sorted by model distance:
  nonbonded pdb=" CD1 LEU G  23 "
            pdb=" OE1 GLU G  56 "
     model   vdw
     1.717 3.460
  nonbonded pdb=" N   GLN G  24 "
            pdb=" OE2 GLU G  56 "
     model   vdw
     2.100 3.120
  nonbonded pdb=" O2   DC I  49 "
            pdb=" N2   DG J 121 "
     model   vdw
     2.194 2.496
  nonbonded pdb=" OG1 THR G  16 "
            pdb=" OP1  DA J  55 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" OG  SER D  84 "
            pdb=" OP1  DG I  38 "
     model   vdw
     2.223 3.040
  ... (remaining 107895 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' and resid 38 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 23 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 13 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 28 through 121)
  selection = (chain 'H' and resid 28 through 121)
}

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 group one per residue
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:             1.460
  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:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.050
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
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   0.069  13264  Z= 0.193
  Angle     :  0.687   8.646  19238  Z= 0.435
  Chirality :  0.038   0.228   2184
  Planarity :  0.005   0.045   1361
  Dihedral  : 27.461  88.908   5745
  Min Nonbonded Distance : 1.717

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  1.10 %
    Favored  : 98.58 %
  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:  0.85 (0.28), residues: 746
  helix:  1.00 (0.20), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.46 (0.40), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  92 
 TYR   0.026   0.002   TYR B  88 
 PHE   0.015   0.002   PHE G  25 
 HIS   0.004   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (13264)
  covalent geometry    : angle       0.68709 (19238)
  hydrogen bonds       : bond        0.09614 (  810)
  hydrogen bonds       : angle       3.85534 ( 2004)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 191
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8407 (tm-30)
REVERT: B   49 LEU cc_start: 0.9175 (mt) cc_final: 0.8924 (mt)
REVERT: B   53 GLU cc_start: 0.8655 (mp0) cc_final: 0.8427 (mp0)
REVERT: C   72 ASP cc_start: 0.8941 (m-30) cc_final: 0.8720 (m-30)
REVERT: C   90 ASP cc_start: 0.8518 (t0) cc_final: 0.8212 (t70)
REVERT: D   42 LEU cc_start: 0.9576 (tp) cc_final: 0.9318 (tp)
REVERT: D   65 ASP cc_start: 0.8916 (t0) cc_final: 0.8545 (t0)
REVERT: E   62 ILE cc_start: 0.9611 (tt) cc_final: 0.9372 (tt)
REVERT: E   74 ILE cc_start: 0.9547 (tt) cc_final: 0.9331 (tt)
REVERT: F   63 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8918 (mp0)
REVERT: G   64 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8473 (tm-30)
REVERT: H   45 VAL cc_start: 0.9002 (t) cc_final: 0.8748 (t)
REVERT: H   65 ASP cc_start: 0.9048 (t70) cc_final: 0.8844 (t0)
REVERT: H   73 GLU cc_start: 0.9031 (tp30) cc_final: 0.8540 (tp30)
  outliers start: 2
  outliers final: 0
  residues processed: 191
  average time/residue: 0.1015
  time to fit residues: 28.3455
Evaluate side-chains
  137 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
B  93 GLN
C  24 GLN
D  44 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.044472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.033416 restraints weight = 133828.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.034129 restraints weight = 62767.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.034483 restraints weight = 39020.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.034787 restraints weight = 31190.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.035057 restraints weight = 26244.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.3458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  13264  Z= 0.233
  Angle     :  0.659   9.859  19238  Z= 0.385
  Chirality :  0.038   0.223   2184
  Planarity :  0.005   0.052   1361
  Dihedral  : 31.720  89.967   4224
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 12.91 %
    Favored  : 84.09 %
  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: 746
  helix:  1.88 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.39 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  40 
 TYR   0.019   0.002   TYR C  50 
 PHE   0.015   0.002   PHE E  67 
 HIS   0.007   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 (13264)
  covalent geometry    : angle       0.65905 (19238)
  hydrogen bonds       : bond        0.04956 (  810)
  hydrogen bonds       : angle       3.41251 ( 2004)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8543 (tm-30)
REVERT: B   25 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.7135 (m110)
REVERT: B   53 GLU cc_start: 0.8998 (mp0) cc_final: 0.8567 (pm20)
REVERT: B   63 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8687 (mp0)
REVERT: B   74 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8327 (mt-10)
REVERT: B   88 TYR cc_start: 0.8923 (m-10) cc_final: 0.8623 (m-10)
REVERT: C   36 LYS cc_start: 0.9592 (ttmt) cc_final: 0.9375 (ttmm)
REVERT: C   61 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8540 (mm-30)
REVERT: C   90 ASP cc_start: 0.8912 (t0) cc_final: 0.8667 (t70)
REVERT: D   65 ASP cc_start: 0.9193 (t0) cc_final: 0.8824 (t0)
REVERT: D   68 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8582 (tm-30)
REVERT: E   61 LEU cc_start: 0.9433 (mp) cc_final: 0.8946 (mt)
REVERT: E   97 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8120 (mt-10)
REVERT: E  120 MET cc_start: 0.8206 (mtm) cc_final: 0.7927 (mpp)
REVERT: G   38 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8047 (t0)
REVERT: G  101 THR cc_start: 0.9537 (m) cc_final: 0.9278 (t)
REVERT: G  104 GLN cc_start: 0.8881 (mp10) cc_final: 0.8555 (pm20)
REVERT: H   65 ASP cc_start: 0.9297 (t70) cc_final: 0.9042 (t0)
REVERT: H   73 GLU cc_start: 0.9291 (tp30) cc_final: 0.8796 (tp30)
  outliers start: 19
  outliers final: 5
  residues processed: 168
  average time/residue: 0.0991
  time to fit residues: 24.6468
Evaluate side-chains
  138 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 129
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 ASN
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain H residue   36 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 96 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 83 optimal weight:    7.9990
   chunk 42 optimal weight:    0.7980
   chunk 99 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  75 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.044463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.033234 restraints weight = 132432.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.033929 restraints weight = 63389.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.034328 restraints weight = 40298.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.034640 restraints weight = 31709.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.034833 restraints weight = 26985.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.3968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13264  Z= 0.166
  Angle     :  0.596   7.489  19238  Z= 0.349
  Chirality :  0.035   0.252   2184
  Planarity :  0.004   0.053   1361
  Dihedral  : 31.466  89.230   4224
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 17.95 %
    Favored  : 80.63 %
  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:  2.36 (0.30), residues: 746
  helix:  2.26 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.46 (0.41), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  23 
 TYR   0.021   0.002   TYR G  39 
 PHE   0.013   0.001   PHE G  25 
 HIS   0.005   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (13264)
  covalent geometry    : angle       0.59596 (19238)
  hydrogen bonds       : bond        0.03894 (  810)
  hydrogen bonds       : angle       3.09506 ( 2004)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 149
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9101 (tt0) cc_final: 0.8600 (tt0)
REVERT: A   94 GLU cc_start: 0.9193 (tp30) cc_final: 0.8880 (tp30)
REVERT: A  105 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8602 (tm-30)
REVERT: B   53 GLU cc_start: 0.8978 (mp0) cc_final: 0.8558 (mp0)
REVERT: B   63 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8590 (mp0)
REVERT: B   74 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8216 (mt-10)
REVERT: B   84 MET cc_start: 0.9361 (mmm) cc_final: 0.9052 (mmm)
REVERT: B   88 TYR cc_start: 0.9012 (m-10) cc_final: 0.8632 (m-10)
REVERT: C   36 LYS cc_start: 0.9580 (ttmt) cc_final: 0.9359 (ttmm)
REVERT: C   64 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8699 (pp20)
REVERT: C   90 ASP cc_start: 0.8843 (t0) cc_final: 0.8626 (t70)
REVERT: D   65 ASP cc_start: 0.9131 (t0) cc_final: 0.8760 (t0)
REVERT: D   68 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8540 (tm-30)
REVERT: E  120 MET cc_start: 0.8190 (mtm) cc_final: 0.7989 (mpp)
REVERT: F   52 GLU cc_start: 0.8532 (pm20) cc_final: 0.8321 (pm20)
REVERT: G   64 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8910 (pp20)
REVERT: G  104 GLN cc_start: 0.8792 (mp10) cc_final: 0.8437 (mp10)
REVERT: H   65 ASP cc_start: 0.9250 (t70) cc_final: 0.9031 (t0)
REVERT: H   73 GLU cc_start: 0.9226 (tp30) cc_final: 0.8840 (tp30)
  outliers start: 9
  outliers final: 5
  residues processed: 152
  average time/residue: 0.1004
  time to fit residues: 22.3681
Evaluate side-chains
  132 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 126
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain H residue   36 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9980
   chunk 11 optimal weight:    5.9990
   chunk 73 optimal weight:    5.9990
   chunk 89 optimal weight:    7.9990
   chunk 40 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9990
   chunk 87 optimal weight:   30.0000
   chunk 8 optimal weight:    0.9980
   chunk 75 optimal weight:    8.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
C  31 HIS
C  38 ASN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.040439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.029292 restraints weight = 134924.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.029917 restraints weight = 65386.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.030215 restraints weight = 42217.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.030491 restraints weight = 34407.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.030688 restraints weight = 29176.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.5515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  13264  Z= 0.234
  Angle     :  0.647  10.320  19238  Z= 0.374
  Chirality :  0.036   0.169   2184
  Planarity :  0.004   0.053   1361
  Dihedral  : 31.840  89.499   4224
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 18.27 %
    Favored  : 77.80 %
  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:  2.21 (0.30), residues: 746
  helix:  2.16 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.58 (0.40), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  71 
 TYR   0.031   0.002   TYR F  88 
 PHE   0.011   0.002   PHE A 104 
 HIS   0.008   0.002   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 (13264)
  covalent geometry    : angle       0.64734 (19238)
  hydrogen bonds       : bond        0.05030 (  810)
  hydrogen bonds       : angle       3.36367 ( 2004)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8659 (tm-30)
REVERT: A  120 MET cc_start: 0.8906 (mmm) cc_final: 0.8660 (mmm)
REVERT: B   53 GLU cc_start: 0.9049 (mp0) cc_final: 0.8636 (mp0)
REVERT: B   74 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8287 (mt-10)
REVERT: B   84 MET cc_start: 0.9315 (mmm) cc_final: 0.8844 (mmm)
REVERT: B   88 TYR cc_start: 0.9074 (m-10) cc_final: 0.8646 (m-10)
REVERT: C   36 LYS cc_start: 0.9605 (ttmt) cc_final: 0.9358 (ttmm)
REVERT: C   38 ASN cc_start: 0.9407 (OUTLIER) cc_final: 0.8555 (t0)
REVERT: C   61 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8595 (mm-30)
REVERT: D   65 ASP cc_start: 0.9181 (t0) cc_final: 0.8853 (t0)
REVERT: D   68 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8644 (tm-30)
REVERT: D   83 ARG cc_start: 0.9096 (tpp80) cc_final: 0.8776 (tpp80)
REVERT: F   63 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8755 (mp0)
REVERT: F   88 TYR cc_start: 0.8645 (m-80) cc_final: 0.8119 (m-80)
REVERT: G   36 LYS cc_start: 0.9266 (mtmm) cc_final: 0.8975 (mtmm)
REVERT: H   65 ASP cc_start: 0.9254 (t70) cc_final: 0.9045 (t0)
REVERT: H   73 GLU cc_start: 0.9282 (tp30) cc_final: 0.8914 (tp30)
REVERT: H   80 TYR cc_start: 0.7372 (m-10) cc_final: 0.6580 (m-10)
  outliers start: 25
  outliers final: 14
  residues processed: 145
  average time/residue: 0.1088
  time to fit residues: 22.8148
Evaluate side-chains
  129 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain E residue   56 LYS
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   51 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 88 optimal weight:   10.0000
   chunk 95 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 90 optimal weight:    8.9990
   chunk 5 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    8.9990
   chunk 20 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 ASN
D  60 ASN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.040642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.029496 restraints weight = 133865.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.030140 restraints weight = 65074.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.030499 restraints weight = 41729.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.030691 restraints weight = 33050.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.030891 restraints weight = 28912.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.5840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13264  Z= 0.183
  Angle     :  0.623  10.056  19238  Z= 0.358
  Chirality :  0.035   0.164   2184
  Planarity :  0.004   0.054   1361
  Dihedral  : 31.611  89.863   4224
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.00 %
    Favored  : 77.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.45 (0.31), residues: 746
  helix:  2.36 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.46 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 116 
 TYR   0.011   0.001   TYR F  88 
 PHE   0.007   0.001   PHE G  25 
 HIS   0.008   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (13264)
  covalent geometry    : angle       0.62268 (19238)
  hydrogen bonds       : bond        0.04059 (  810)
  hydrogen bonds       : angle       3.17696 ( 2004)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8650 (tm-30)
REVERT: A  120 MET cc_start: 0.8927 (mmm) cc_final: 0.8640 (mmm)
REVERT: B   53 GLU cc_start: 0.9032 (mp0) cc_final: 0.8613 (mp0)
REVERT: B   63 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8649 (mp0)
REVERT: B   74 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8212 (mt-10)
REVERT: B   84 MET cc_start: 0.9370 (mmm) cc_final: 0.8913 (mmm)
REVERT: B   88 TYR cc_start: 0.9049 (m-10) cc_final: 0.8617 (m-10)
REVERT: C   38 ASN cc_start: 0.9367 (OUTLIER) cc_final: 0.8546 (t0)
REVERT: C   61 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8431 (mm-30)
REVERT: D   65 ASP cc_start: 0.9129 (t0) cc_final: 0.8817 (t0)
REVERT: D   68 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8601 (tm-30)
REVERT: D   83 ARG cc_start: 0.9104 (tpp80) cc_final: 0.8732 (tpp80)
REVERT: D  105 LYS cc_start: 0.9268 (ptpt) cc_final: 0.8990 (ptpp)
REVERT: E   65 LEU cc_start: 0.9854 (OUTLIER) cc_final: 0.9534 (mm)
REVERT: E  120 MET cc_start: 0.7899 (mpp) cc_final: 0.7616 (mpp)
REVERT: F   52 GLU cc_start: 0.8627 (pm20) cc_final: 0.7876 (pm20)
REVERT: F   88 TYR cc_start: 0.8692 (m-80) cc_final: 0.7959 (m-80)
REVERT: G   36 LYS cc_start: 0.9258 (mtmm) cc_final: 0.8774 (mtmm)
REVERT: G   56 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8545 (mm-30)
REVERT: G   64 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8963 (pp20)
REVERT: H   73 GLU cc_start: 0.9287 (tp30) cc_final: 0.8893 (tp30)
REVERT: H   80 TYR cc_start: 0.7354 (m-10) cc_final: 0.6587 (m-10)
REVERT: H  102 GLU cc_start: 0.8564 (tp30) cc_final: 0.8263 (tp30)
  outliers start: 19
  outliers final: 6
  residues processed: 141
  average time/residue: 0.1012
  time to fit residues: 21.0409
Evaluate side-chains
  131 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   58 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 81 optimal weight:    7.9990
   chunk 58 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 96 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9990
   chunk 75 optimal weight:    7.9990
   chunk 83 optimal weight:    7.9990
   chunk 80 optimal weight:    8.9990
   chunk 36 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
C  38 ASN
** D  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 113 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.037764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2538 r_free = 0.2538 target = 0.026725 restraints weight = 140407.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2574 r_free = 0.2574 target = 0.027289 restraints weight = 70622.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2592 r_free = 0.2592 target = 0.027571 restraints weight = 46358.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.027837 restraints weight = 37902.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.027980 restraints weight = 32262.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.2550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.7030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.080  13264  Z= 0.311
  Angle     :  0.715  11.719  19238  Z= 0.407
  Chirality :  0.038   0.163   2184
  Planarity :  0.005   0.051   1361
  Dihedral  : 32.269  89.807   4224
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 22.99 %
    Favored  : 74.17 %
  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:  2.02 (0.30), residues: 746
  helix:  2.12 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.85 (0.39), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  71 
 TYR   0.014   0.002   TYR C  50 
 PHE   0.014   0.002   PHE D  62 
 HIS   0.007   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00692 (13264)
  covalent geometry    : angle       0.71471 (19238)
  hydrogen bonds       : bond        0.06528 (  810)
  hydrogen bonds       : angle       3.69458 ( 2004)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8518 (tm-30)
REVERT: B   53 GLU cc_start: 0.9053 (mp0) cc_final: 0.8674 (mp0)
REVERT: B   63 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8694 (mp0)
REVERT: B   74 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8286 (mt-10)
REVERT: B   88 TYR cc_start: 0.9063 (m-10) cc_final: 0.8618 (m-10)
REVERT: C   61 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8606 (mp0)
REVERT: D   65 ASP cc_start: 0.9216 (t0) cc_final: 0.8982 (t0)
REVERT: D   68 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8673 (tm-30)
REVERT: D   83 ARG cc_start: 0.9212 (tpp80) cc_final: 0.8786 (tpp80)
REVERT: D  105 LYS cc_start: 0.9214 (ptpt) cc_final: 0.9002 (ptpt)
REVERT: E   50 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.9051 (pp20)
REVERT: E  105 GLU cc_start: 0.8882 (tp30) cc_final: 0.8624 (tm-30)
REVERT: G   36 LYS cc_start: 0.9302 (mtmm) cc_final: 0.8799 (mtmm)
REVERT: H  102 GLU cc_start: 0.8450 (tp30) cc_final: 0.8068 (tp30)
  outliers start: 18
  outliers final: 11
  residues processed: 131
  average time/residue: 0.0915
  time to fit residues: 17.9546
Evaluate side-chains
  129 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain E residue   50 GLU
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain H residue   99 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 91 optimal weight:    7.9990
   chunk 93 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0030
   chunk 38 optimal weight:    8.9990
   chunk 58 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   chunk 79 optimal weight:    6.9990
   chunk 73 optimal weight:    8.9990
   chunk 99 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    1.5594

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
D  60 ASN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.039215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2590 r_free = 0.2590 target = 0.028255 restraints weight = 135675.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.028859 restraints weight = 66879.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.029172 restraints weight = 43138.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.029329 restraints weight = 34858.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.029572 restraints weight = 30965.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.7045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13264  Z= 0.175
  Angle     :  0.650  10.440  19238  Z= 0.369
  Chirality :  0.035   0.154   2184
  Planarity :  0.004   0.055   1361
  Dihedral  : 31.736  89.869   4224
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 23.94 %
    Favored  : 73.70 %
  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:  2.24 (0.31), residues: 746
  helix:  2.26 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.70 (0.40), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  36 
 TYR   0.018   0.002   TYR F  88 
 PHE   0.006   0.001   PHE A  78 
 HIS   0.006   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (13264)
  covalent geometry    : angle       0.64964 (19238)
  hydrogen bonds       : bond        0.04059 (  810)
  hydrogen bonds       : angle       3.21320 ( 2004)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8607 (tm-30)
REVERT: A  120 MET cc_start: 0.8764 (mmm) cc_final: 0.8317 (mmm)
REVERT: B   53 GLU cc_start: 0.8951 (mp0) cc_final: 0.8535 (mp0)
REVERT: B   63 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8639 (mp0)
REVERT: B   74 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8197 (mt-10)
REVERT: B   88 TYR cc_start: 0.9074 (m-10) cc_final: 0.8644 (m-10)
REVERT: C   61 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8602 (mm-30)
REVERT: D   83 ARG cc_start: 0.9202 (tpp80) cc_final: 0.8986 (tpp80)
REVERT: E   50 GLU cc_start: 0.9270 (pt0) cc_final: 0.8912 (pp20)
REVERT: E   65 LEU cc_start: 0.9834 (OUTLIER) cc_final: 0.9515 (mm)
REVERT: E  105 GLU cc_start: 0.8946 (tp30) cc_final: 0.8632 (tm-30)
REVERT: G   36 LYS cc_start: 0.9310 (mtmm) cc_final: 0.8815 (mtmm)
REVERT: H   73 GLU cc_start: 0.9189 (tp30) cc_final: 0.8636 (tp30)
  outliers start: 15
  outliers final: 6
  residues processed: 143
  average time/residue: 0.1038
  time to fit residues: 21.8619
Evaluate side-chains
  123 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain H residue   91 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 89 optimal weight:    8.9990
   chunk 82 optimal weight:    7.9990
   chunk 69 optimal weight:    0.8980
   chunk 76 optimal weight:    7.9990
   chunk 75 optimal weight:    7.9990
   chunk 86 optimal weight:   20.0000
   chunk 98 optimal weight:    5.9990
   chunk 33 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 65 optimal weight:    0.1980
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.039367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.028346 restraints weight = 135647.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.028962 restraints weight = 67451.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.029311 restraints weight = 42786.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.029518 restraints weight = 33850.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.029666 restraints weight = 29438.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.2608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8704
moved from start:          0.7155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13264  Z= 0.173
  Angle     :  0.667  12.454  19238  Z= 0.375
  Chirality :  0.034   0.161   2184
  Planarity :  0.004   0.055   1361
  Dihedral  : 31.568  87.875   4224
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 24.88 %
    Favored  : 72.28 %
  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:  2.21 (0.31), residues: 746
  helix:  2.20 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.61 (0.41), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 134 
 TYR   0.013   0.001   TYR F  88 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.008   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (13264)
  covalent geometry    : angle       0.66674 (19238)
  hydrogen bonds       : bond        0.04048 (  810)
  hydrogen bonds       : angle       3.19611 ( 2004)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9139 (tp30) cc_final: 0.8860 (tp30)
REVERT: A   97 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8276 (mt-10)
REVERT: A  105 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8552 (tm-30)
REVERT: A  120 MET cc_start: 0.8845 (mmm) cc_final: 0.8431 (mmm)
REVERT: B   53 GLU cc_start: 0.8900 (mp0) cc_final: 0.8484 (mp0)
REVERT: B   63 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8602 (mp0)
REVERT: B   74 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8106 (mt-10)
REVERT: B   88 TYR cc_start: 0.9069 (m-10) cc_final: 0.8562 (m-10)
REVERT: C   61 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8509 (mm-30)
REVERT: D   83 ARG cc_start: 0.9198 (tpp80) cc_final: 0.8975 (tpp80)
REVERT: D  105 LYS cc_start: 0.9320 (ptpt) cc_final: 0.9117 (ptpp)
REVERT: E   50 GLU cc_start: 0.9266 (pt0) cc_final: 0.8899 (pp20)
REVERT: E   65 LEU cc_start: 0.9842 (OUTLIER) cc_final: 0.9524 (mm)
REVERT: E  105 GLU cc_start: 0.8984 (tp30) cc_final: 0.8670 (tm-30)
REVERT: F   88 TYR cc_start: 0.8624 (m-80) cc_final: 0.5975 (m-80)
REVERT: G   36 LYS cc_start: 0.9320 (mtmm) cc_final: 0.8819 (mtmm)
REVERT: G   56 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8342 (mm-30)
  outliers start: 18
  outliers final: 9
  residues processed: 143
  average time/residue: 0.1048
  time to fit residues: 21.8508
Evaluate side-chains
  128 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain H residue   99 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 88 optimal weight:   10.0000
   chunk 67 optimal weight:    0.9990
   chunk 92 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 34 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 64 optimal weight:    7.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.038558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2572 r_free = 0.2572 target = 0.027708 restraints weight = 137818.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.028281 restraints weight = 66480.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.028607 restraints weight = 42671.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.028768 restraints weight = 34063.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.028915 restraints weight = 30101.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.2571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8742
moved from start:          0.7489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  13264  Z= 0.216
  Angle     :  0.688  12.765  19238  Z= 0.388
  Chirality :  0.036   0.241   2184
  Planarity :  0.004   0.057   1361
  Dihedral  : 31.756  88.905   4224
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 25.51 %
    Favored  : 71.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.19 (0.31), residues: 746
  helix:  2.20 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.63 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  71 
 TYR   0.011   0.001   TYR C  50 
 PHE   0.007   0.001   PHE A  67 
 HIS   0.006   0.001   HIS H  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 (13264)
  covalent geometry    : angle       0.68782 (19238)
  hydrogen bonds       : bond        0.04562 (  810)
  hydrogen bonds       : angle       3.29569 ( 2004)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8598 (tm-30)
REVERT: A  120 MET cc_start: 0.8873 (mmm) cc_final: 0.8489 (mmm)
REVERT: B   53 GLU cc_start: 0.8942 (mp0) cc_final: 0.8546 (mp0)
REVERT: B   63 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8623 (mp0)
REVERT: B   74 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8206 (mt-10)
REVERT: B   84 MET cc_start: 0.9306 (mmm) cc_final: 0.8852 (mmm)
REVERT: B   88 TYR cc_start: 0.9075 (m-10) cc_final: 0.8578 (m-10)
REVERT: C   61 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8482 (mp0)
REVERT: C  104 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8894 (mm-40)
REVERT: D   83 ARG cc_start: 0.9226 (tpp80) cc_final: 0.9001 (tpp80)
REVERT: D  105 LYS cc_start: 0.9250 (ptpt) cc_final: 0.8963 (ptpp)
REVERT: E   50 GLU cc_start: 0.9297 (pt0) cc_final: 0.8991 (pp20)
REVERT: E   65 LEU cc_start: 0.9850 (OUTLIER) cc_final: 0.9545 (mm)
REVERT: E   94 GLU cc_start: 0.9215 (tp30) cc_final: 0.8413 (tp30)
REVERT: E   97 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8160 (mp0)
REVERT: E  105 GLU cc_start: 0.9012 (tp30) cc_final: 0.8733 (tm-30)
REVERT: G   36 LYS cc_start: 0.9316 (mtmm) cc_final: 0.8886 (mtmm)
REVERT: G   56 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8227 (mm-30)
  outliers start: 16
  outliers final: 11
  residues processed: 126
  average time/residue: 0.1042
  time to fit residues: 19.4717
Evaluate side-chains
  121 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 94 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 75 optimal weight:    7.9990
   chunk 23 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 86 optimal weight:   10.0000
   chunk 56 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.039368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2605 r_free = 0.2605 target = 0.028490 restraints weight = 136748.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2642 r_free = 0.2642 target = 0.029097 restraints weight = 66034.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.029433 restraints weight = 42168.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.029693 restraints weight = 33559.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.029778 restraints weight = 28431.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.2608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8706
moved from start:          0.7540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13264  Z= 0.168
  Angle     :  0.683  14.094  19238  Z= 0.382
  Chirality :  0.035   0.232   2184
  Planarity :  0.004   0.062   1361
  Dihedral  : 31.428  88.128   4224
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 25.98 %
    Favored  : 71.50 %
  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:  2.21 (0.30), residues: 746
  helix:  2.21 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.62 (0.42), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  95 
 TYR   0.009   0.001   TYR F  88 
 PHE   0.008   0.001   PHE A  67 
 HIS   0.007   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (13264)
  covalent geometry    : angle       0.68299 (19238)
  hydrogen bonds       : bond        0.03952 (  810)
  hydrogen bonds       : angle       3.10612 ( 2004)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8589 (tm-30)
REVERT: A  120 MET cc_start: 0.8824 (mmm) cc_final: 0.8441 (mmm)
REVERT: B   53 GLU cc_start: 0.8895 (mp0) cc_final: 0.8480 (mp0)
REVERT: B   59 LYS cc_start: 0.9117 (tppp) cc_final: 0.8601 (ttmm)
REVERT: B   63 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8592 (mp0)
REVERT: B   74 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8078 (mt-10)
REVERT: B   88 TYR cc_start: 0.9086 (m-10) cc_final: 0.8619 (m-10)
REVERT: C   61 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8521 (mm-30)
REVERT: C  104 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8822 (mm-40)
REVERT: D   83 ARG cc_start: 0.9207 (tpp80) cc_final: 0.8963 (tpp80)
REVERT: D  105 LYS cc_start: 0.9239 (ptpt) cc_final: 0.8943 (ptpp)
REVERT: E   50 GLU cc_start: 0.9287 (pt0) cc_final: 0.8858 (pp20)
REVERT: E   65 LEU cc_start: 0.9838 (OUTLIER) cc_final: 0.9524 (mm)
REVERT: E   94 GLU cc_start: 0.9218 (tp30) cc_final: 0.8949 (tp30)
REVERT: E  105 GLU cc_start: 0.9045 (tp30) cc_final: 0.8739 (tm-30)
REVERT: F   63 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8256 (mt-10)
REVERT: F   84 MET cc_start: 0.9118 (tpp) cc_final: 0.8514 (tpp)
REVERT: G   36 LYS cc_start: 0.9320 (mtmm) cc_final: 0.8874 (mtmm)
REVERT: G   56 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8358 (mm-30)
REVERT: H   73 GLU cc_start: 0.9184 (tp30) cc_final: 0.8642 (tp30)
  outliers start: 16
  outliers final: 9
  residues processed: 128
  average time/residue: 0.1011
  time to fit residues: 19.1125
Evaluate side-chains
  124 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain F residue   88 TYR
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   58 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 79 optimal weight:    7.9990
   chunk 44 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.039627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.028831 restraints weight = 135508.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.029440 restraints weight = 66632.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.029764 restraints weight = 42963.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.030049 restraints weight = 34532.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.030114 restraints weight = 29174.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8686
moved from start:          0.7607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13264  Z= 0.163
  Angle     :  0.670  13.805  19238  Z= 0.375
  Chirality :  0.034   0.231   2184
  Planarity :  0.004   0.060   1361
  Dihedral  : 31.379  88.816   4224
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 26.46 %
    Favored  : 71.18 %
  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:  2.28 (0.30), residues: 746
  helix:  2.26 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.60 (0.42), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  95 
 TYR   0.010   0.001   TYR F  88 
 PHE   0.008   0.001   PHE A  67 
 HIS   0.007   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (13264)
  covalent geometry    : angle       0.66984 (19238)
  hydrogen bonds       : bond        0.03948 (  810)
  hydrogen bonds       : angle       3.07405 ( 2004)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1885.36 seconds
wall clock time: 33 minutes 8.92 seconds (1988.92 seconds total)