Starting phenix.real_space_refine
on Wed Jul 30 09:08:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y00_33536/07_2025/7y00_33536.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y00_33536/07_2025/7y00_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y00_33536/07_2025/7y00_33536.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y00_33536/07_2025/7y00_33536.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y00_33536/07_2025/7y00_33536.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y00_33536/07_2025/7y00_33536.cif"
  }
  resolution = 3.96
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.42, per 1000 atoms: 0.60
  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: 2.83
  Conformation dependent library (CDL) restraints added in 899.1 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: 5.82
  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: 4.39

  Time building geometry restraints manager: 3.43 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:             1.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.500
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     33.210
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.710
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (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
 HIS   0.004   0.001   HIS E 113 
 PHE   0.015   0.002   PHE G  25 
 TYR   0.026   0.002   TYR B  88 
 ARG   0.005   0.001   ARG B  92 

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

*********************** 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  : 0.872 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8406 (tm-30)
REVERT: B   49 LEU cc_start: 0.9175 (mt) cc_final: 0.8923 (mt)
REVERT: B   53 GLU cc_start: 0.8655 (mp0) cc_final: 0.8427 (mp0)
REVERT: C   90 ASP cc_start: 0.8518 (t0) cc_final: 0.8211 (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: 0.8542 (t0)
REVERT: E   62 ILE cc_start: 0.9611 (tt) cc_final: 0.9371 (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: 0.9003 (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: 0.2267
  time to fit residues: 62.5014
Evaluate side-chains
  136 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 79 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 59 optimal weight:    6.9990
   chunk 92 optimal weight:    7.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 ASN
C  24 GLN
C  38 ASN
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 = 0.3424 r_free = 0.3424 target = 0.051397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.040443 restraints weight = 130086.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.041241 restraints weight = 62627.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.041697 restraints weight = 39271.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13264  Z= 0.161
  Angle     :  0.605   7.794  19238  Z= 0.354
  Chirality :  0.035   0.204   2184
  Planarity :  0.005   0.057   1361
  Dihedral  : 31.060  88.571   4224
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 12.91 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.30), residues: 746
  helix:  2.10 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.38 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS A 113 
 PHE   0.012   0.001   PHE E  67 
 TYR   0.021   0.002   TYR C  50 
 ARG   0.006   0.000   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04077 (  810)
  hydrogen bonds       : angle       3.14819 ( 2004)
  covalent geometry    : bond        0.00348 (13264)
  covalent geometry    : angle       0.60459 (19238)

*********************** 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
  180 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 168
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8546 (tm-30)
REVERT: B   49 LEU cc_start: 0.9329 (mt) cc_final: 0.8713 (mt)
REVERT: B   53 GLU cc_start: 0.8870 (mp0) cc_final: 0.8495 (mp0)
REVERT: B   63 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8591 (mp0)
REVERT: B   88 TYR cc_start: 0.8878 (m-10) cc_final: 0.8540 (m-10)
REVERT: C   36 LYS cc_start: 0.9517 (ttmt) cc_final: 0.9312 (ttmm)
REVERT: C   90 ASP cc_start: 0.8817 (t0) cc_final: 0.8544 (t70)
REVERT: D   65 ASP cc_start: 0.9143 (t0) cc_final: 0.8734 (t0)
REVERT: D   68 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8467 (tm-30)
REVERT: E   61 LEU cc_start: 0.9395 (mp) cc_final: 0.9143 (mp)
REVERT: E   97 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8558 (mt-10)
REVERT: F   93 GLN cc_start: 0.9351 (tp40) cc_final: 0.9108 (tp40)
REVERT: G   64 GLU cc_start: 0.9169 (tm-30) cc_final: 0.8873 (tm-30)
REVERT: H   65 ASP cc_start: 0.9344 (t70) cc_final: 0.9095 (t0)
REVERT: H   73 GLU cc_start: 0.9169 (tp30) cc_final: 0.8797 (tp30)
REVERT: H   80 TYR cc_start: 0.7704 (m-10) cc_final: 0.6515 (m-10)
  outliers start: 12
  outliers final: 3
  residues processed: 175
  average time/residue: 0.2266
  time to fit residues: 58.4214
Evaluate side-chains
  140 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 136
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain G residue   78 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 95 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 74 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 96 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 9 optimal weight:    0.4980
   chunk 33 optimal weight:    0.7980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3317 r_free = 0.3317 target = 0.047258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.036103 restraints weight = 132299.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.036876 restraints weight = 63411.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.037335 restraints weight = 39595.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.3194

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= 0.165
  Angle     :  0.593   9.759  19238  Z= 0.345
  Chirality :  0.035   0.183   2184
  Planarity :  0.004   0.056   1361
  Dihedral  : 31.408  89.035   4224
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 14.33 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.30), residues: 746
  helix:  2.26 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.30 (0.42), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS A 113 
 PHE   0.027   0.002   PHE E  67 
 TYR   0.045   0.002   TYR F  88 
 ARG   0.005   0.000   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03923 (  810)
  hydrogen bonds       : angle       3.01713 ( 2004)
  covalent geometry    : bond        0.00359 (13264)
  covalent geometry    : angle       0.59272 (19238)

*********************** 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
  187 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 165
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.9052 (tt0) cc_final: 0.8178 (tt0)
REVERT: A   90 MET cc_start: 0.9404 (mmm) cc_final: 0.9185 (mmm)
REVERT: A  105 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8660 (tm-30)
REVERT: B   53 GLU cc_start: 0.9032 (mp0) cc_final: 0.8632 (pm20)
REVERT: B   63 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8710 (mp0)
REVERT: B   88 TYR cc_start: 0.9018 (m-10) cc_final: 0.8662 (m-10)
REVERT: C   36 LYS cc_start: 0.9591 (ttmt) cc_final: 0.9378 (ttmm)
REVERT: C   61 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8514 (mm-30)
REVERT: C   64 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8807 (pp20)
REVERT: C   90 ASP cc_start: 0.8818 (t0) cc_final: 0.8532 (t70)
REVERT: D   65 ASP cc_start: 0.9166 (t0) cc_final: 0.8760 (t0)
REVERT: D   68 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8593 (tm-30)
REVERT: D   83 ARG cc_start: 0.8956 (tpp80) cc_final: 0.8519 (tpp80)
REVERT: E  109 LEU cc_start: 0.9480 (tp) cc_final: 0.9240 (tp)
REVERT: E  120 MET cc_start: 0.7606 (mpp) cc_final: 0.7270 (mpp)
REVERT: F   53 GLU cc_start: 0.9394 (OUTLIER) cc_final: 0.9073 (mp0)
REVERT: F   93 GLN cc_start: 0.9407 (tp40) cc_final: 0.9199 (tp40)
REVERT: G  104 GLN cc_start: 0.8808 (mp10) cc_final: 0.8371 (mp10)
REVERT: H   65 ASP cc_start: 0.9356 (t70) cc_final: 0.9114 (t0)
REVERT: H   73 GLU cc_start: 0.9289 (tp30) cc_final: 0.8874 (tp30)
REVERT: H  102 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8662 (tp30)
  outliers start: 22
  outliers final: 7
  residues processed: 171
  average time/residue: 0.2296
  time to fit residues: 57.2939
Evaluate side-chains
  143 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   64 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   53 GLU
Chi-restraints excluded: chain G residue  101 THR
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 78 optimal weight:    7.9990
   chunk 55 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 87 optimal weight:   30.0000
   chunk 99 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 84 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9980
   chunk 80 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  31 HIS
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  75 HIS
G  38 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.040037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2615 r_free = 0.2615 target = 0.028777 restraints weight = 135907.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.029414 restraints weight = 66502.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.029778 restraints weight = 42812.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.2606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.5621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  13264  Z= 0.272
  Angle     :  0.677  13.413  19238  Z= 0.393
  Chirality :  0.038   0.208   2184
  Planarity :  0.005   0.053   1361
  Dihedral  : 32.027  89.917   4224
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.48 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.31), residues: 746
  helix:  2.02 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.52 (0.41), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS B  75 
 PHE   0.018   0.003   PHE E  67 
 TYR   0.031   0.003   TYR F  88 
 ARG   0.005   0.001   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05788 (  810)
  hydrogen bonds       : angle       3.61762 ( 2004)
  covalent geometry    : bond        0.00585 (13264)
  covalent geometry    : angle       0.67700 (19238)

*********************** 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
  152 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 1.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8342 (mt-10)
REVERT: A  105 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8616 (tm-30)
REVERT: A  120 MET cc_start: 0.8980 (mmm) cc_final: 0.8773 (mmm)
REVERT: B   34 ILE cc_start: 0.9773 (mt) cc_final: 0.9509 (tt)
REVERT: B   53 GLU cc_start: 0.9061 (mp0) cc_final: 0.8732 (mp0)
REVERT: B   63 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8707 (mp0)
REVERT: B   84 MET cc_start: 0.9378 (mmm) cc_final: 0.9012 (mmm)
REVERT: B   88 TYR cc_start: 0.9100 (m-10) cc_final: 0.8718 (m-10)
REVERT: C   36 LYS cc_start: 0.9599 (ttmt) cc_final: 0.9358 (ttmm)
REVERT: C   61 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8428 (mp0)
REVERT: C   64 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8854 (pp20)
REVERT: D   65 ASP cc_start: 0.9214 (t0) cc_final: 0.8891 (t0)
REVERT: D   68 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8671 (tm-30)
REVERT: D   83 ARG cc_start: 0.9096 (tpp80) cc_final: 0.8673 (tpp80)
REVERT: E   76 GLN cc_start: 0.8998 (mp10) cc_final: 0.8656 (mp10)
REVERT: E   97 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8157 (mt-10)
REVERT: E  120 MET cc_start: 0.8075 (mpp) cc_final: 0.7639 (mpp)
REVERT: F   88 TYR cc_start: 0.8863 (m-80) cc_final: 0.8277 (m-80)
REVERT: G   38 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.8604 (t0)
REVERT: G   56 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8315 (mm-30)
REVERT: G   64 GLU cc_start: 0.9303 (tm-30) cc_final: 0.8963 (pp20)
REVERT: G   72 ASP cc_start: 0.8947 (m-30) cc_final: 0.8737 (p0)
REVERT: G  104 GLN cc_start: 0.8918 (mp10) cc_final: 0.8633 (mp10)
REVERT: H   65 ASP cc_start: 0.9235 (t70) cc_final: 0.9001 (t0)
  outliers start: 19
  outliers final: 11
  residues processed: 146
  average time/residue: 0.2819
  time to fit residues: 59.5429
Evaluate side-chains
  128 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
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   22 LEU
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   81 VAL
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 E residue   62 ILE
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue  101 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 98 optimal weight:    6.9990
   chunk 79 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 101 optimal weight:    8.9990
   chunk 100 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
F  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.040579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2632 r_free = 0.2632 target = 0.029395 restraints weight = 133782.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.030044 restraints weight = 64517.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.030383 restraints weight = 41387.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.5935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13264  Z= 0.184
  Angle     :  0.624  11.640  19238  Z= 0.361
  Chirality :  0.035   0.148   2184
  Planarity :  0.004   0.052   1361
  Dihedral  : 31.663  89.863   4224
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 21.57 %
    Favored  : 75.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.31), residues: 746
  helix:  2.29 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -0.49 (0.41), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.018   0.001   PHE E  67 
 TYR   0.024   0.001   TYR H  80 
 ARG   0.003   0.000   ARG E 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04049 (  810)
  hydrogen bonds       : angle       3.17860 ( 2004)
  covalent geometry    : bond        0.00407 (13264)
  covalent geometry    : angle       0.62445 (19238)

*********************** 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
  146 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8692 (tm-30)
REVERT: A  120 MET cc_start: 0.8965 (mmm) cc_final: 0.8696 (mmm)
REVERT: B   34 ILE cc_start: 0.9758 (mt) cc_final: 0.9492 (tt)
REVERT: B   53 GLU cc_start: 0.9097 (mp0) cc_final: 0.8744 (mp0)
REVERT: B   63 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8664 (mp0)
REVERT: B   84 MET cc_start: 0.9358 (mmm) cc_final: 0.9006 (mmm)
REVERT: B   88 TYR cc_start: 0.9049 (m-10) cc_final: 0.8649 (m-10)
REVERT: C   61 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8602 (mm-30)
REVERT: C   64 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8752 (pp20)
REVERT: D   65 ASP cc_start: 0.9170 (t0) cc_final: 0.8865 (t0)
REVERT: D   68 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8603 (tm-30)
REVERT: D   83 ARG cc_start: 0.9095 (tpp80) cc_final: 0.8702 (tpp80)
REVERT: D  105 LYS cc_start: 0.9265 (mtmm) cc_final: 0.8955 (pttm)
REVERT: E  105 GLU cc_start: 0.8947 (tp30) cc_final: 0.8663 (tm-30)
REVERT: E  120 MET cc_start: 0.8183 (mpp) cc_final: 0.7825 (mpp)
REVERT: F   63 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8735 (mp0)
REVERT: F   88 TYR cc_start: 0.8424 (m-10) cc_final: 0.8003 (m-80)
REVERT: G   56 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8235 (mm-30)
REVERT: G   64 GLU cc_start: 0.9254 (tm-30) cc_final: 0.9043 (pp20)
REVERT: G  104 GLN cc_start: 0.8956 (mp10) cc_final: 0.8453 (mp10)
REVERT: H   73 GLU cc_start: 0.9202 (tp30) cc_final: 0.8674 (tp30)
REVERT: H   80 TYR cc_start: 0.7520 (m-80) cc_final: 0.6480 (m-10)
REVERT: H  102 GLU cc_start: 0.8711 (tp30) cc_final: 0.8394 (tp30)
  outliers start: 18
  outliers final: 8
  residues processed: 138
  average time/residue: 0.2367
  time to fit residues: 47.5471
Evaluate side-chains
  123 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
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   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 E residue   62 ILE
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain G residue  101 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 95 optimal weight:    6.9990
   chunk 54 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 93 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9990
   chunk 101 optimal weight:    8.9990
   chunk 20 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 18 optimal weight:    0.0000
   overall best weight:    1.7992

-------------------------------------------------------------------------------
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 = 0.3124 r_free = 0.3124 target = 0.040279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.029110 restraints weight = 136080.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.029772 restraints weight = 65705.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.030145 restraints weight = 41622.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.6259

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= 0.183
  Angle     :  0.626  13.095  19238  Z= 0.358
  Chirality :  0.034   0.160   2184
  Planarity :  0.004   0.052   1361
  Dihedral  : 31.602  88.964   4224
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 21.42 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.31), residues: 746
  helix:  2.38 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.43 (0.42), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 113 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.013   0.001   TYR H  80 
 ARG   0.004   0.000   ARG E 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04153 (  810)
  hydrogen bonds       : angle       3.16093 ( 2004)
  covalent geometry    : bond        0.00406 (13264)
  covalent geometry    : angle       0.62639 (19238)

*********************** 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
  147 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8678 (tm-30)
REVERT: A  120 MET cc_start: 0.8964 (mmm) cc_final: 0.8672 (mmm)
REVERT: B   34 ILE cc_start: 0.9743 (mt) cc_final: 0.9468 (tt)
REVERT: B   53 GLU cc_start: 0.9111 (mp0) cc_final: 0.8750 (mp0)
REVERT: B   59 LYS cc_start: 0.9161 (tppp) cc_final: 0.8734 (tppt)
REVERT: B   63 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8679 (mp0)
REVERT: B   84 MET cc_start: 0.9369 (mmm) cc_final: 0.9019 (mmm)
REVERT: B   88 TYR cc_start: 0.9053 (m-10) cc_final: 0.8615 (m-10)
REVERT: C   61 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8590 (mm-30)
REVERT: D   65 ASP cc_start: 0.9168 (t0) cc_final: 0.8835 (t0)
REVERT: D   68 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8649 (tm-30)
REVERT: D   83 ARG cc_start: 0.9118 (tpp80) cc_final: 0.8692 (tpp80)
REVERT: D  105 LYS cc_start: 0.9292 (mtmm) cc_final: 0.9021 (pttm)
REVERT: E   50 GLU cc_start: 0.9327 (pt0) cc_final: 0.9020 (pp20)
REVERT: E   65 LEU cc_start: 0.9856 (OUTLIER) cc_final: 0.9524 (mm)
REVERT: E  105 GLU cc_start: 0.8999 (tp30) cc_final: 0.8675 (tm-30)
REVERT: E  120 MET cc_start: 0.8202 (mpp) cc_final: 0.7908 (mpp)
REVERT: F   59 LYS cc_start: 0.9554 (tttm) cc_final: 0.8830 (tptm)
REVERT: F   63 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8621 (mt-10)
REVERT: F   88 TYR cc_start: 0.8561 (m-10) cc_final: 0.7977 (m-80)
REVERT: G   56 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8251 (mm-30)
REVERT: G   61 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8698 (mm-30)
REVERT: G   64 GLU cc_start: 0.9327 (tm-30) cc_final: 0.9102 (pp20)
REVERT: G  104 GLN cc_start: 0.8891 (mp10) cc_final: 0.8350 (mp10)
REVERT: H   80 TYR cc_start: 0.7531 (m-80) cc_final: 0.6509 (m-10)
REVERT: H  102 GLU cc_start: 0.8461 (tp30) cc_final: 0.8065 (tp30)
  outliers start: 16
  outliers final: 10
  residues processed: 141
  average time/residue: 0.2427
  time to fit residues: 49.0359
Evaluate side-chains
  133 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
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   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 E residue   62 ILE
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 90 optimal weight:    8.9990
   chunk 49 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   chunk 68 optimal weight:    8.9990
   chunk 20 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 9 optimal weight:    0.4980
   chunk 44 optimal weight:    0.0020
   chunk 39 optimal weight:    4.9990
   chunk 3 optimal weight:    0.4980
   overall best weight:    0.5388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.041613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.030612 restraints weight = 133461.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.031268 restraints weight = 64368.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.031686 restraints weight = 41121.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.6342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13264  Z= 0.150
  Angle     :  0.610  12.134  19238  Z= 0.351
  Chirality :  0.033   0.155   2184
  Planarity :  0.004   0.053   1361
  Dihedral  : 31.183  88.658   4224
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 22.05 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.31), residues: 746
  helix:  2.33 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.38 (0.42), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 113 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.009   0.001   TYR G  39 
 ARG   0.003   0.000   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03771 (  810)
  hydrogen bonds       : angle       2.95829 ( 2004)
  covalent geometry    : bond        0.00326 (13264)
  covalent geometry    : angle       0.61035 (19238)

*********************** 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
  150 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 1.027 
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: A   93 GLN cc_start: 0.9034 (tt0) cc_final: 0.8571 (tm-30)
REVERT: A   97 GLU cc_start: 0.8668 (mt-10) cc_final: 0.7818 (mt-10)
REVERT: A  105 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8634 (tm-30)
REVERT: A  120 MET cc_start: 0.8880 (mmm) cc_final: 0.8619 (mmm)
REVERT: B   34 ILE cc_start: 0.9733 (mt) cc_final: 0.9418 (tt)
REVERT: B   53 GLU cc_start: 0.9073 (mp0) cc_final: 0.8727 (mp0)
REVERT: B   59 LYS cc_start: 0.9080 (tppp) cc_final: 0.8737 (ttmm)
REVERT: B   63 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8674 (mp0)
REVERT: B   84 MET cc_start: 0.9388 (mmm) cc_final: 0.9049 (mmm)
REVERT: B   88 TYR cc_start: 0.9026 (m-10) cc_final: 0.8621 (m-10)
REVERT: C   61 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8489 (mm-30)
REVERT: C   64 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8853 (pp20)
REVERT: D   68 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8568 (tm-30)
REVERT: D   83 ARG cc_start: 0.9073 (tpp80) cc_final: 0.8644 (tpp80)
REVERT: E   50 GLU cc_start: 0.9269 (pt0) cc_final: 0.8937 (pp20)
REVERT: E  105 GLU cc_start: 0.9030 (tp30) cc_final: 0.8705 (tm-30)
REVERT: E  120 MET cc_start: 0.8193 (mpp) cc_final: 0.7965 (mtt)
REVERT: F   88 TYR cc_start: 0.8521 (m-10) cc_final: 0.7912 (m-80)
REVERT: G   56 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8252 (mm-30)
REVERT: G   64 GLU cc_start: 0.9283 (tm-30) cc_final: 0.9022 (pp20)
REVERT: G  104 GLN cc_start: 0.8692 (mp10) cc_final: 0.8492 (mp10)
REVERT: H   73 GLU cc_start: 0.9073 (tp30) cc_final: 0.8605 (tp30)
REVERT: H   80 TYR cc_start: 0.7370 (m-80) cc_final: 0.6299 (m-10)
REVERT: H  102 GLU cc_start: 0.8377 (tp30) cc_final: 0.8102 (tp30)
  outliers start: 11
  outliers final: 3
  residues processed: 146
  average time/residue: 0.2539
  time to fit residues: 53.1768
Evaluate side-chains
  128 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 123
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
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   63 GLU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   61 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 80 optimal weight:   10.0000
   chunk 96 optimal weight:    7.9990
   chunk 54 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0980
   chunk 11 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 101 optimal weight:   10.0000
   chunk 57 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 88 optimal weight:   10.0000
   overall best weight:    1.5986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.040566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.029507 restraints weight = 134725.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.030157 restraints weight = 65349.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.030612 restraints weight = 41608.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.6618

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= 0.174
  Angle     :  0.628  12.463  19238  Z= 0.357
  Chirality :  0.034   0.158   2184
  Planarity :  0.004   0.052   1361
  Dihedral  : 31.446  87.934   4224
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 22.36 %
    Favored  : 75.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (0.31), residues: 746
  helix:  2.41 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.42 (0.42), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E 113 
 PHE   0.042   0.002   PHE E  67 
 TYR   0.011   0.001   TYR H  80 
 ARG   0.002   0.000   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04017 (  810)
  hydrogen bonds       : angle       3.12881 ( 2004)
  covalent geometry    : bond        0.00386 (13264)
  covalent geometry    : angle       0.62784 (19238)

*********************** 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
  141 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8665 (tm-30)
REVERT: B   34 ILE cc_start: 0.9735 (mt) cc_final: 0.9471 (tt)
REVERT: B   53 GLU cc_start: 0.9112 (mp0) cc_final: 0.8775 (mp0)
REVERT: B   59 LYS cc_start: 0.9123 (tppp) cc_final: 0.8710 (ttmm)
REVERT: B   63 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8654 (mp0)
REVERT: B   84 MET cc_start: 0.9347 (mmm) cc_final: 0.9001 (mmm)
REVERT: B   88 TYR cc_start: 0.9014 (m-10) cc_final: 0.8577 (m-10)
REVERT: C   61 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8419 (mp0)
REVERT: C   64 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8836 (pp20)
REVERT: D   68 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8633 (tm-30)
REVERT: D   83 ARG cc_start: 0.9100 (tpp80) cc_final: 0.8711 (tpp80)
REVERT: D  105 LYS cc_start: 0.9193 (mtmm) cc_final: 0.8954 (pttm)
REVERT: E   59 GLU cc_start: 0.8411 (pm20) cc_final: 0.8174 (pm20)
REVERT: E   65 LEU cc_start: 0.9842 (OUTLIER) cc_final: 0.9533 (mm)
REVERT: E  105 GLU cc_start: 0.9005 (tp30) cc_final: 0.8710 (tm-30)
REVERT: E  120 MET cc_start: 0.8290 (mpp) cc_final: 0.8007 (mtt)
REVERT: F   53 GLU cc_start: 0.9209 (mp0) cc_final: 0.8977 (mp0)
REVERT: F   88 TYR cc_start: 0.8520 (m-10) cc_final: 0.7720 (m-80)
REVERT: G   56 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8251 (mm-30)
REVERT: G  104 GLN cc_start: 0.8708 (mp10) cc_final: 0.8504 (mp10)
REVERT: H   73 GLU cc_start: 0.9169 (tp30) cc_final: 0.8610 (tp30)
REVERT: H   80 TYR cc_start: 0.7401 (m-80) cc_final: 0.6436 (m-10)
REVERT: H  102 GLU cc_start: 0.8405 (tp30) cc_final: 0.8073 (tp30)
  outliers start: 15
  outliers final: 8
  residues processed: 136
  average time/residue: 0.2426
  time to fit residues: 48.1894
Evaluate side-chains
  133 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
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   63 GLU
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   61 GLU
Chi-restraints excluded: chain E residue   62 ILE
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 74 optimal weight:    8.9990
   chunk 3 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 85 optimal weight:   10.0000
   chunk 90 optimal weight:    8.9990
   chunk 79 optimal weight:    7.9990
   chunk 73 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.040077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.029084 restraints weight = 134017.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.029688 restraints weight = 65577.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.030030 restraints weight = 42070.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.2615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.6909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13264  Z= 0.180
  Angle     :  0.652  11.643  19238  Z= 0.367
  Chirality :  0.034   0.252   2184
  Planarity :  0.004   0.055   1361
  Dihedral  : 31.464  87.721   4224
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 23.94 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.31), residues: 746
  helix:  2.32 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.43 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.050   0.002   PHE E  67 
 TYR   0.012   0.001   TYR H  80 
 ARG   0.002   0.000   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04088 (  810)
  hydrogen bonds       : angle       3.20501 ( 2004)
  covalent geometry    : bond        0.00402 (13264)
  covalent geometry    : angle       0.65184 (19238)

*********************** 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: 10
    poor density    : 120
  time to evaluate  : 0.904 
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   94 GLU cc_start: 0.9004 (tp30) cc_final: 0.8319 (tp30)
REVERT: A   97 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8471 (mt-10)
REVERT: A  105 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8646 (tm-30)
REVERT: B   34 ILE cc_start: 0.9730 (mt) cc_final: 0.9459 (tt)
REVERT: B   53 GLU cc_start: 0.9121 (mp0) cc_final: 0.8786 (mp0)
REVERT: B   59 LYS cc_start: 0.9120 (tppp) cc_final: 0.8777 (ttmm)
REVERT: B   63 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8647 (mp0)
REVERT: B   84 MET cc_start: 0.9316 (mmm) cc_final: 0.8975 (mmm)
REVERT: B   88 TYR cc_start: 0.9042 (m-10) cc_final: 0.8596 (m-10)
REVERT: C   61 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8381 (mm-30)
REVERT: C   64 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8846 (pp20)
REVERT: D   68 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8645 (tm-30)
REVERT: D   83 ARG cc_start: 0.9176 (tpp80) cc_final: 0.8925 (tpp80)
REVERT: E   50 GLU cc_start: 0.9232 (pp20) cc_final: 0.8928 (pp20)
REVERT: E   65 LEU cc_start: 0.9828 (OUTLIER) cc_final: 0.9510 (mm)
REVERT: E  105 GLU cc_start: 0.9030 (tp30) cc_final: 0.8706 (tm-30)
REVERT: E  120 MET cc_start: 0.8340 (mpp) cc_final: 0.8028 (mtt)
REVERT: F   88 TYR cc_start: 0.8538 (m-10) cc_final: 0.7674 (m-80)
REVERT: G   23 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9249 (mm)
REVERT: G   56 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8305 (mm-30)
REVERT: G  104 GLN cc_start: 0.8743 (mp10) cc_final: 0.8301 (mp10)
REVERT: H   73 GLU cc_start: 0.9175 (tp30) cc_final: 0.8615 (tp30)
REVERT: H   80 TYR cc_start: 0.7415 (m-80) cc_final: 0.6510 (m-10)
REVERT: H  102 GLU cc_start: 0.8544 (tp30) cc_final: 0.8177 (tp30)
  outliers start: 10
  outliers final: 5
  residues processed: 127
  average time/residue: 0.2567
  time to fit residues: 47.2341
Evaluate side-chains
  126 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   61 GLU
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 98 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   chunk 76 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 97 optimal weight:    7.9990
   chunk 31 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.9388

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.039661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.028661 restraints weight = 135331.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.029296 restraints weight = 64968.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.029613 restraints weight = 41402.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.7201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  13264  Z= 0.189
  Angle     :  0.666  11.790  19238  Z= 0.375
  Chirality :  0.035   0.257   2184
  Planarity :  0.004   0.056   1361
  Dihedral  : 31.527  87.715   4224
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 24.09 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.30), residues: 746
  helix:  2.26 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.42 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.050   0.002   PHE E  67 
 TYR   0.013   0.001   TYR H  80 
 ARG   0.002   0.000   ARG F  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04199 (  810)
  hydrogen bonds       : angle       3.24794 ( 2004)
  covalent geometry    : bond        0.00425 (13264)
  covalent geometry    : angle       0.66600 (19238)

********************** 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: 12
    poor density    : 122
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9071 (tp30) cc_final: 0.8480 (tp30)
REVERT: A   97 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8461 (mt-10)
REVERT: A  105 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8624 (tm-30)
REVERT: A  120 MET cc_start: 0.8928 (mmm) cc_final: 0.8488 (mmm)
REVERT: B   34 ILE cc_start: 0.9737 (mt) cc_final: 0.9453 (tt)
REVERT: B   53 GLU cc_start: 0.9090 (mp0) cc_final: 0.8767 (mp0)
REVERT: B   59 LYS cc_start: 0.9103 (tppp) cc_final: 0.8768 (ttmm)
REVERT: B   63 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8658 (mp0)
REVERT: B   84 MET cc_start: 0.9286 (mmm) cc_final: 0.8949 (mmm)
REVERT: B   88 TYR cc_start: 0.9039 (m-10) cc_final: 0.8601 (m-10)
REVERT: C   61 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8404 (mp0)
REVERT: C   64 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8834 (pp20)
REVERT: D   68 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8581 (tm-30)
REVERT: D   83 ARG cc_start: 0.9173 (tpp80) cc_final: 0.8907 (tpp80)
REVERT: E   50 GLU cc_start: 0.9217 (pp20) cc_final: 0.8945 (pp20)
REVERT: E   65 LEU cc_start: 0.9812 (OUTLIER) cc_final: 0.9525 (mm)
REVERT: E  105 GLU cc_start: 0.8983 (tp30) cc_final: 0.8682 (tm-30)
REVERT: E  120 MET cc_start: 0.8327 (mpp) cc_final: 0.8043 (mtt)
REVERT: F   88 TYR cc_start: 0.8589 (m-10) cc_final: 0.7672 (m-80)
REVERT: G   23 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9249 (mm)
REVERT: G   56 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8280 (mm-30)
REVERT: G   72 ASP cc_start: 0.8915 (m-30) cc_final: 0.8697 (p0)
REVERT: G  104 GLN cc_start: 0.8699 (mp10) cc_final: 0.8310 (mp10)
REVERT: H   73 GLU cc_start: 0.9155 (tp30) cc_final: 0.8582 (tp30)
REVERT: H   80 TYR cc_start: 0.7433 (m-80) cc_final: 0.6541 (m-10)
REVERT: H  102 GLU cc_start: 0.8421 (tp30) cc_final: 0.8023 (tp30)
  outliers start: 12
  outliers final: 8
  residues processed: 131
  average time/residue: 0.2441
  time to fit residues: 45.5825
Evaluate side-chains
  129 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
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   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 E residue   65 LEU
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  114 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 69 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 89 optimal weight:    8.9990
   chunk 78 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.040494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.029515 restraints weight = 134451.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.030165 restraints weight = 64674.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.030528 restraints weight = 40999.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8678
moved from start:          0.7275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13264  Z= 0.159
  Angle     :  0.660  11.878  19238  Z= 0.369
  Chirality :  0.034   0.242   2184
  Planarity :  0.004   0.058   1361
  Dihedral  : 31.244  88.706   4224
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 25.04 %
    Favored  : 73.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.30), residues: 746
  helix:  2.19 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.37 (0.41), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS F  75 
 PHE   0.050   0.002   PHE E  67 
 TYR   0.010   0.001   TYR D  34 
 ARG   0.002   0.000   ARG E  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03885 (  810)
  hydrogen bonds       : angle       3.21133 ( 2004)
  covalent geometry    : bond        0.00351 (13264)
  covalent geometry    : angle       0.65969 (19238)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3851.83 seconds
wall clock time: 68 minutes 59.35 seconds (4139.35 seconds total)