Starting phenix.real_space_refine
on Wed Feb 12 12:53:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sat_24956/02_2025/7sat_24956.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sat_24956/02_2025/7sat_24956.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sat_24956/02_2025/7sat_24956.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sat_24956/02_2025/7sat_24956.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sat_24956/02_2025/7sat_24956.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sat_24956/02_2025/7sat_24956.cif"
  }
  resolution = 3.9
  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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1811 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    4255      2.51       5
     N    1111      2.21       5
     O    1174      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6581
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1704
          Classifications: {'peptide': 219}
          Link IDs: {'PTRANS': 3, 'TRANS': 215}
    Chain: "B"
      Number of atoms: 1688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1688
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 3, 'TRANS': 214}
    Chain: "C"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 638
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "D"
      Number of atoms: 612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 612
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 2, 'TRANS': 71}
    Chain: "E"
      Number of atoms: 663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 663
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 2, 'TRANS': 77}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 638
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "G"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 638
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
  Time building chain proxies: 4.28, per 1000 atoms: 0.65
  Number of scatterers: 6581
  At special positions: 0
  Unit cell: (86.508, 84.372, 130.296, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      41     16.00
     O    1174      8.00
     N    1111      7.00
     C    4255      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: 1.59
  Conformation dependent library (CDL) restraints added in 923.4 milliseconds
  

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1534

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 0 sheets defined
      74.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 26
    Processing helix  chain 'A' and resid 31 through 70
      removed outlier: 3.610A  pdb=" N   SER A  44 " --> pdb=" O   LYS A  40 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   SER A  61 " --> pdb=" O   ASN A  57 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   GLU A  62 " --> pdb=" O   LEU A  58 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU A  63 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 107
    Processing helix  chain 'A' and resid 125 through 130
    Processing helix  chain 'A' and resid 135 through 148
      removed outlier: 4.317A  pdb=" N   THR A 139 " --> pdb=" O   GLY A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 155
      removed outlier: 3.665A  pdb=" N   MET A 155 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 167
      removed outlier: 4.626A  pdb=" N   GLN A 166 " --> pdb=" O   LYS A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 223
    Processing helix  chain 'B' and resid 10 through 31
      removed outlier: 4.024A  pdb=" N   MET B  14 " --> pdb=" O   ASN B  10 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   LEU B  20 " --> pdb=" O   ASN B  16 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   VAL B  21 " --> pdb=" O   LEU B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 70
      removed outlier: 3.932A  pdb=" N   LYS B  40 " --> pdb=" O   ASP B  36 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL B  41 " --> pdb=" O   GLY B  37 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   THR B  69 " --> pdb=" O   THR B  65 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ASN B  70 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 98
    Processing helix  chain 'B' and resid 100 through 105
      removed outlier: 4.037A  pdb=" N   GLU B 105 " --> pdb=" O   ALA B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 130
    Processing helix  chain 'B' and resid 136 through 154
      removed outlier: 4.219A  pdb=" N   LYS B 146 " --> pdb=" O   LYS B 142 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   PHE B 147 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU B 154 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 168
    Processing helix  chain 'B' and resid 178 through 183
    Processing helix  chain 'B' and resid 188 through 221
    Processing helix  chain 'C' and resid 3 through 16
      removed outlier: 3.577A  pdb=" N   ALA C  16 " --> pdb=" O   GLU C  12 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 45
      removed outlier: 3.897A  pdb=" N   LEU C  23 " --> pdb=" O   LYS C  19 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ASN C  25 " --> pdb=" O   ARG C  21 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ILE C  26 " --> pdb=" O   ARG C  22 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 67
      removed outlier: 3.659A  pdb=" N   MET C  52 " --> pdb=" O   MET C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 68 through 70
      No H-bonds generated for 'chain 'C' and resid 68 through 70'
    Processing helix  chain 'D' and resid 8 through 17
    Processing helix  chain 'D' and resid 19 through 43
      removed outlier: 3.903A  pdb=" N   LEU D  23 " --> pdb=" O   LYS D  19 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 68
      removed outlier: 3.964A  pdb=" N   MET D  52 " --> pdb=" O   MET D  48 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU D  53 " --> pdb=" O   GLY D  49 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   PHE D  54 " --> pdb=" O   ASN D  50 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 7 through 17
      removed outlier: 3.735A  pdb=" N   MET E  13 " --> pdb=" O   ASN E   9 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   TYR E  14 " --> pdb=" O   ILE E  10 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU E  15 " --> pdb=" O   LEU E  11 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 17 through 44
    Processing helix  chain 'E' and resid 49 through 67
      removed outlier: 3.951A  pdb=" N   VAL E  55 " --> pdb=" O   GLU E  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 68 through 70
      No H-bonds generated for 'chain 'E' and resid 68 through 70'
    Processing helix  chain 'F' and resid 3 through 15
      removed outlier: 3.669A  pdb=" N   TYR F   7 " --> pdb=" O   HIS F   3 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 17 through 44
      removed outlier: 3.998A  pdb=" N   ALA F  32 " --> pdb=" O   TYR F  28 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 67
      removed outlier: 3.594A  pdb=" N   PHE F  54 " --> pdb=" O   ASN F  50 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 11 through 16
      removed outlier: 3.562A  pdb=" N   ALA G  16 " --> pdb=" O   GLU G  12 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 45
      removed outlier: 3.526A  pdb=" N   LEU G  23 " --> pdb=" O   LYS G  19 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 49 through 67

    441 hydrogen bonds defined for protein.
    1314 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.78

  Time building geometry restraints manager: 1.81 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: 2077
        1.34 -     1.46: 1008
        1.46 -     1.57: 3545
        1.57 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 6710
  Sorted by residual:
  bond pdb=" CG  GLU B 209 "
       pdb=" CD  GLU B 209 "
    ideal  model  delta    sigma   weight residual
    1.516  1.489  0.027 2.50e-02 1.60e+03 1.21e+00
  bond pdb=" CG1 ILE B  15 "
       pdb=" CD1 ILE B  15 "
    ideal  model  delta    sigma   weight residual
    1.513  1.471  0.042 3.90e-02 6.57e+02 1.14e+00
  bond pdb=" CA  VAL B 151 "
       pdb=" C   VAL B 151 "
    ideal  model  delta    sigma   weight residual
    1.518  1.530 -0.012 1.13e-02 7.83e+03 1.10e+00
  bond pdb=" CB  VAL D  63 "
       pdb=" CG1 VAL D  63 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.05e+00
  bond pdb=" CB  VAL C  35 "
       pdb=" CG1 VAL C  35 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 9.97e-01
  ... (remaining 6705 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 8814
        2.09 -     4.19: 184
        4.19 -     6.28: 27
        6.28 -     8.37: 8
        8.37 -    10.46: 1
  Bond angle restraints: 9034
  Sorted by residual:
  angle pdb=" N   TRP G  30 "
        pdb=" CA  TRP G  30 "
        pdb=" CB  TRP G  30 "
      ideal   model   delta    sigma   weight residual
     110.39  116.53   -6.14 1.66e+00 3.63e-01 1.37e+01
  angle pdb=" C   ARG A 148 "
        pdb=" N   GLU A 149 "
        pdb=" CA  GLU A 149 "
      ideal   model   delta    sigma   weight residual
     121.54  128.46   -6.92 1.91e+00 2.74e-01 1.31e+01
  angle pdb=" C   SER G  29 "
        pdb=" N   TRP G  30 "
        pdb=" CA  TRP G  30 "
      ideal   model   delta    sigma   weight residual
     120.72  114.85    5.87 1.67e+00 3.59e-01 1.24e+01
  angle pdb=" N   ARG B 117 "
        pdb=" CA  ARG B 117 "
        pdb=" C   ARG B 117 "
      ideal   model   delta    sigma   weight residual
     113.43  109.25    4.18 1.26e+00 6.30e-01 1.10e+01
  angle pdb=" N   ASP A 115 "
        pdb=" CA  ASP A 115 "
        pdb=" C   ASP A 115 "
      ideal   model   delta    sigma   weight residual
     114.64  109.78    4.86 1.52e+00 4.33e-01 1.02e+01
  ... (remaining 9029 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.04: 3380
       14.04 -    28.08: 450
       28.08 -    42.12: 151
       42.12 -    56.16: 23
       56.16 -    70.20: 10
  Dihedral angle restraints: 4014
    sinusoidal: 1632
      harmonic: 2382
  Sorted by residual:
  dihedral pdb=" CA  LYS B  99 "
           pdb=" C   LYS B  99 "
           pdb=" N   LEU B 100 "
           pdb=" CA  LEU B 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.88   22.12     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" CA  TRP A 179 "
           pdb=" C   TRP A 179 "
           pdb=" N   GLU A 180 "
           pdb=" CA  GLU A 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.09   18.91     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  LEU B 161 "
           pdb=" C   LEU B 161 "
           pdb=" N   LYS B 162 "
           pdb=" CA  LYS B 162 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.84  -18.16     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 4011 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 818
       0.048 -    0.097: 169
       0.097 -    0.145: 21
       0.145 -    0.194: 3
       0.194 -    0.242: 1
  Chirality restraints: 1012
  Sorted by residual:
  chirality pdb=" CA  TRP G  30 "
            pdb=" N   TRP G  30 "
            pdb=" C   TRP G  30 "
            pdb=" CB  TRP G  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  GLU A  87 "
            pdb=" N   GLU A  87 "
            pdb=" C   GLU A  87 "
            pdb=" CB  GLU A  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.71e-01
  chirality pdb=" CB  ILE A  15 "
            pdb=" CA  ILE A  15 "
            pdb=" CG1 ILE A  15 "
            pdb=" CG2 ILE A  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.35e-01
  ... (remaining 1009 not shown)

  Planarity restraints: 1122
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP G  30 "    0.039 2.00e-02 2.50e+03   3.50e-02 3.07e+01
        pdb=" CG  TRP G  30 "   -0.094 2.00e-02 2.50e+03
        pdb=" CD1 TRP G  30 "    0.041 2.00e-02 2.50e+03
        pdb=" CD2 TRP G  30 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP G  30 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP G  30 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP G  30 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP G  30 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP G  30 "    0.013 2.00e-02 2.50e+03
        pdb=" CH2 TRP G  30 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU E  46 "   -0.053 5.00e-02 4.00e+02   8.06e-02 1.04e+01
        pdb=" N   PRO E  47 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO E  47 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO E  47 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  83 "   -0.012 2.00e-02 2.50e+03   2.43e-02 5.89e+00
        pdb=" C   VAL A  83 "    0.042 2.00e-02 2.50e+03
        pdb=" O   VAL A  83 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LEU A  84 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1119 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 111
        2.64 -     3.21: 6605
        3.21 -     3.77: 10371
        3.77 -     4.34: 13204
        4.34 -     4.90: 21473
  Nonbonded interactions: 51764
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 181 "
            pdb=" OE1 GLU A 185 "
     model   vdw
     2.080 3.040
  nonbonded pdb=" OD1 ASN A  64 "
            pdb=" OH  TYR A  78 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" O   VAL F  63 "
            pdb=" OG  SER F  67 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" NZ  LYS A  99 "
            pdb=" OE1 GLN A 200 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" O   ASP B  89 "
            pdb=" OG1 THR B  93 "
     model   vdw
     2.264 3.040
  ... (remaining 51759 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' and resid 5 through 221)
  selection = (chain 'B' and resid 5 through 221)
}
ncs_group {
  reference = (chain 'C' and resid 5 through 78)
  selection = chain 'D'
  selection = (chain 'E' and resid 5 through 78)
  selection = (chain 'F' and resid 5 through 78)
  selection = (chain 'G' and resid 5 through 78)
}

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=1.00 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:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.030
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
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   0.042   6710  Z= 0.254
  Angle     :  0.755  10.464   9034  Z= 0.409
  Chirality :  0.040   0.242   1012
  Planarity :  0.004   0.081   1122
  Dihedral  : 14.441  70.198   2480
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 15.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  0.14 %
    Favored  : 99.58 %
  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:  0.06 (0.30), residues: 808
  helix:  1.09 (0.22), residues: 573
  sheet:  None (None), residues: 0
  loop : -2.67 (0.39), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.094   0.003   TRP G  30 
 HIS   0.009   0.001   HIS C  18 
 PHE   0.019   0.001   PHE D  61 
 TYR   0.025   0.002   TYR D   7 
 ARG   0.009   0.001   ARG D  21 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 281
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ASP cc_start: 0.8054 (p0) cc_final: 0.7736 (p0)
REVERT: A  194 THR cc_start: 0.8510 (m) cc_final: 0.7855 (m)
REVERT: A  204 ARG cc_start: 0.8811 (mmt-90) cc_final: 0.8458 (tpp-160)
REVERT: C   12 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7126 (tm-30)
REVERT: C   13 MET cc_start: 0.7482 (ptp) cc_final: 0.7097 (ptp)
REVERT: D   48 MET cc_start: 0.6970 (ptt) cc_final: 0.6593 (ptt)
REVERT: G   51 GLU cc_start: 0.8387 (mp0) cc_final: 0.8174 (mp0)
  outliers start: 2
  outliers final: 0
  residues processed: 281
  average time/residue: 0.1947
  time to fit residues: 70.4896
Evaluate side-chains
  235 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:   10.0000
   chunk 59 optimal weight:    3.9990
   chunk 32 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 39 optimal weight:    0.0970
   chunk 31 optimal weight:    4.9990
   chunk 61 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0270
   chunk 45 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.5636

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

Flipped N/Q/H residues before XYZ refinement:
A   6 ASN
** B  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  29 ASN
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.121794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.096629 restraints weight = 13196.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.099174 restraints weight = 7957.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.101069 restraints weight = 5720.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6710  Z= 0.194
  Angle     :  0.705  11.984   9034  Z= 0.357
  Chirality :  0.039   0.154   1012
  Planarity :  0.004   0.055   1122
  Dihedral  :  4.558  20.021    888
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 14.08 %
    Favored  : 83.52 %
  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:  0.34 (0.30), residues: 808
  helix:  1.25 (0.21), residues: 595
  sheet:  None (None), residues: 0
  loop : -2.83 (0.42), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.002   TRP G  30 
 HIS   0.005   0.001   HIS C  18 
 PHE   0.022   0.002   PHE D  54 
 TYR   0.017   0.002   TYR B 205 
 ARG   0.006   0.001   ARG B  80 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 262
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 ARG cc_start: 0.8730 (mmt-90) cc_final: 0.7772 (tpp-160)
REVERT: B   78 TYR cc_start: 0.6838 (t80) cc_final: 0.6571 (t80)
REVERT: B  155 MET cc_start: 0.1437 (mmt) cc_final: 0.0766 (mmt)
REVERT: C   12 GLU cc_start: 0.7321 (tm-30) cc_final: 0.7119 (tm-30)
REVERT: C   13 MET cc_start: 0.7410 (ptp) cc_final: 0.7012 (ptp)
REVERT: C   24 LEU cc_start: 0.9034 (mt) cc_final: 0.8405 (tp)
REVERT: C   60 GLU cc_start: 0.8512 (pp20) cc_final: 0.8024 (pp20)
REVERT: D   48 MET cc_start: 0.6885 (ptt) cc_final: 0.6661 (ptt)
REVERT: E   17 SER cc_start: 0.7251 (m) cc_final: 0.6944 (p)
REVERT: E   22 ARG cc_start: 0.7909 (ttt-90) cc_final: 0.7658 (tpt-90)
REVERT: G   14 TYR cc_start: 0.7833 (t80) cc_final: 0.7630 (t80)
REVERT: G   30 TRP cc_start: 0.8389 (m-90) cc_final: 0.8085 (m-90)
REVERT: G   74 MET cc_start: 0.7280 (mmm) cc_final: 0.7078 (mmm)
  outliers start: 17
  outliers final: 13
  residues processed: 269
  average time/residue: 0.1941
  time to fit residues: 67.3020
Evaluate side-chains
  247 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 234
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   61 SER
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  129 MET
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain F residue   57 MET
Chi-restraints excluded: chain G residue   26 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 48 optimal weight:    0.3980
   chunk 31 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B   6 ASN
B  12 GLN
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.122452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.097025 restraints weight = 13427.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.099570 restraints weight = 8087.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.101309 restraints weight = 5761.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6710  Z= 0.185
  Angle     :  0.685  11.703   9034  Z= 0.341
  Chirality :  0.038   0.143   1012
  Planarity :  0.003   0.051   1122
  Dihedral  :  4.335  19.453    888
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.32 %
    Favored  : 79.58 %
  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:  0.54 (0.30), residues: 808
  helix:  1.48 (0.21), residues: 590
  sheet:  None (None), residues: 0
  loop : -2.91 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.001   TRP G  30 
 HIS   0.003   0.001   HIS E  77 
 PHE   0.024   0.002   PHE D  61 
 TYR   0.019   0.002   TYR A  78 
 ARG   0.006   0.000   ARG G  21 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 266
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LYS cc_start: 0.8320 (tttt) cc_final: 0.8056 (mtpt)
REVERT: A   30 VAL cc_start: 0.8479 (m) cc_final: 0.7843 (t)
REVERT: A  118 ARG cc_start: 0.8266 (ppt170) cc_final: 0.7978 (ppt170)
REVERT: A  204 ARG cc_start: 0.8753 (mmt-90) cc_final: 0.7822 (tpp-160)
REVERT: B   80 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7374 (ptt90)
REVERT: B  155 MET cc_start: 0.1136 (mmt) cc_final: 0.0923 (mmt)
REVERT: C   12 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7200 (tm-30)
REVERT: C   13 MET cc_start: 0.7541 (ptp) cc_final: 0.7139 (ptp)
REVERT: C   60 GLU cc_start: 0.8417 (pp20) cc_final: 0.8003 (pp20)
REVERT: D   37 LEU cc_start: 0.9196 (tt) cc_final: 0.8887 (tt)
REVERT: E   17 SER cc_start: 0.7220 (m) cc_final: 0.6967 (p)
REVERT: E   22 ARG cc_start: 0.7877 (ttt-90) cc_final: 0.7604 (tpt-90)
REVERT: E   74 MET cc_start: 0.7805 (tpp) cc_final: 0.7580 (tpp)
REVERT: F   76 TYR cc_start: 0.7529 (t80) cc_final: 0.7138 (t80)
  outliers start: 22
  outliers final: 15
  residues processed: 278
  average time/residue: 0.1945
  time to fit residues: 69.6910
Evaluate side-chains
  257 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 241
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 GLU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  129 MET
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain B residue    6 ASN
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   80 ARG
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain F residue   57 MET
Chi-restraints excluded: chain G residue   19 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 44 optimal weight:    0.5980
   chunk 68 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 46 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 49 optimal weight:    7.9990
   chunk 56 optimal weight:    7.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 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 = 0.3664 r_free = 0.3664 target = 0.120974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.095320 restraints weight = 13552.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.097890 restraints weight = 8212.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.099683 restraints weight = 5877.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6710  Z= 0.217
  Angle     :  0.691  12.033   9034  Z= 0.349
  Chirality :  0.039   0.158   1012
  Planarity :  0.004   0.049   1122
  Dihedral  :  4.332  19.029    888
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 18.73 %
    Favored  : 77.32 %
  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:  0.56 (0.30), residues: 808
  helix:  1.49 (0.21), residues: 589
  sheet:  None (None), residues: 0
  loop : -2.87 (0.41), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP G  30 
 HIS   0.003   0.001   HIS D  77 
 PHE   0.024   0.002   PHE D  61 
 TYR   0.037   0.002   TYR B  78 
 ARG   0.006   0.000   ARG E  21 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 257
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
REVERT: A  118 ARG cc_start: 0.8233 (ppt170) cc_final: 0.7988 (ppt170)
REVERT: A  194 THR cc_start: 0.8442 (m) cc_final: 0.8209 (m)
REVERT: A  204 ARG cc_start: 0.8789 (mmt-90) cc_final: 0.7824 (tpp-160)
REVERT: B   78 TYR cc_start: 0.7048 (t80) cc_final: 0.6421 (t80)
REVERT: C   12 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7185 (tm-30)
REVERT: C   13 MET cc_start: 0.7487 (ptp) cc_final: 0.7106 (ptp)
REVERT: C   25 ASN cc_start: 0.9113 (t0) cc_final: 0.8841 (m-40)
REVERT: C   52 MET cc_start: 0.8108 (tpp) cc_final: 0.7842 (tpp)
REVERT: C   60 GLU cc_start: 0.8320 (pp20) cc_final: 0.8100 (pp20)
REVERT: D   37 LEU cc_start: 0.9197 (tt) cc_final: 0.8961 (tt)
REVERT: E   17 SER cc_start: 0.7157 (m) cc_final: 0.6932 (p)
REVERT: E   22 ARG cc_start: 0.7940 (ttt-90) cc_final: 0.7562 (tpt-90)
REVERT: F   28 TYR cc_start: 0.6724 (OUTLIER) cc_final: 0.6370 (m-80)
REVERT: F   37 LEU cc_start: 0.8958 (tp) cc_final: 0.8540 (tp)
REVERT: F   70 GLU cc_start: 0.7090 (pm20) cc_final: 0.6604 (mp0)
  outliers start: 28
  outliers final: 23
  residues processed: 271
  average time/residue: 0.1978
  time to fit residues: 69.0354
Evaluate side-chains
  257 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 233
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   29 ASN
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   61 SER
Chi-restraints excluded: chain A residue   87 GLU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  129 MET
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  165 GLU
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain D residue   48 MET
Chi-restraints excluded: chain E residue   15 LEU
Chi-restraints excluded: chain F residue   28 TYR
Chi-restraints excluded: chain F residue   57 MET
Chi-restraints excluded: chain G residue   19 LYS
Chi-restraints excluded: chain G residue   53 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0670
   chunk 51 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 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 = 0.3694 r_free = 0.3694 target = 0.123051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.097409 restraints weight = 13371.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.100031 restraints weight = 8162.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.101802 restraints weight = 5857.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6710  Z= 0.185
  Angle     :  0.706  15.504   9034  Z= 0.350
  Chirality :  0.039   0.183   1012
  Planarity :  0.003   0.045   1122
  Dihedral  :  4.286  19.111    888
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 21.83 %
    Favored  : 74.93 %
  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:  0.64 (0.30), residues: 808
  helix:  1.54 (0.21), residues: 590
  sheet:  None (None), residues: 0
  loop : -2.84 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.002   TRP G  30 
 HIS   0.002   0.000   HIS D  77 
 PHE   0.020   0.002   PHE D  61 
 TYR   0.020   0.002   TYR C   4 
 ARG   0.006   0.000   ARG E  21 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 262
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   78 TYR cc_start: 0.7136 (t80) cc_final: 0.6606 (t80)
REVERT: B  117 ARG cc_start: 0.7493 (ptm-80) cc_final: 0.7041 (ttp-110)
REVERT: B  198 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8067 (pttp)
REVERT: C   12 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7225 (tm-30)
REVERT: C   13 MET cc_start: 0.7583 (ptp) cc_final: 0.7184 (ptp)
REVERT: C   25 ASN cc_start: 0.9085 (t0) cc_final: 0.8796 (m-40)
REVERT: C   60 GLU cc_start: 0.8252 (pp20) cc_final: 0.7933 (pp20)
REVERT: D   37 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8929 (tt)
REVERT: E   17 SER cc_start: 0.7135 (m) cc_final: 0.6925 (p)
REVERT: E   22 ARG cc_start: 0.7888 (ttt-90) cc_final: 0.7548 (tpt-90)
REVERT: E   30 TRP cc_start: 0.8741 (m100) cc_final: 0.8425 (m100)
REVERT: E   67 SER cc_start: 0.8852 (t) cc_final: 0.8563 (p)
REVERT: F   25 ASN cc_start: 0.8678 (t0) cc_final: 0.8453 (t0)
REVERT: F   28 TYR cc_start: 0.6559 (OUTLIER) cc_final: 0.6266 (m-80)
REVERT: F   37 LEU cc_start: 0.8972 (tp) cc_final: 0.8453 (tp)
  outliers start: 23
  outliers final: 16
  residues processed: 274
  average time/residue: 0.2055
  time to fit residues: 71.9143
Evaluate side-chains
  263 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 244
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   61 SER
Chi-restraints excluded: chain A residue   87 GLU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   48 MET
Chi-restraints excluded: chain E residue   15 LEU
Chi-restraints excluded: chain F residue   28 TYR
Chi-restraints excluded: chain F residue   57 MET
Chi-restraints excluded: chain G residue   19 LYS
Chi-restraints excluded: chain G residue   53 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 50 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   chunk 74 optimal weight:    0.7980
   chunk 56 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   chunk 43 optimal weight:    0.5980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.121718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.096147 restraints weight = 13179.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.098612 restraints weight = 8043.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.100428 restraints weight = 5808.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6710  Z= 0.224
  Angle     :  0.731  12.679   9034  Z= 0.365
  Chirality :  0.040   0.169   1012
  Planarity :  0.004   0.046   1122
  Dihedral  :  4.344  18.924    888
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 22.11 %
    Favored  : 73.94 %
  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:  0.58 (0.30), residues: 808
  helix:  1.48 (0.21), residues: 590
  sheet:  None (None), residues: 0
  loop : -2.79 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.079   0.002   TRP G  30 
 HIS   0.003   0.001   HIS D  77 
 PHE   0.020   0.002   PHE D  61 
 TYR   0.020   0.002   TYR E  28 
 ARG   0.006   0.001   ARG D  21 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 255
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
REVERT: B   14 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8388 (tpt)
REVERT: B   78 TYR cc_start: 0.7197 (t80) cc_final: 0.6700 (t80)
REVERT: B  198 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8120 (pttp)
REVERT: C   12 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7233 (tm-30)
REVERT: C   13 MET cc_start: 0.7492 (ptp) cc_final: 0.7104 (ptp)
REVERT: C   25 ASN cc_start: 0.9039 (t0) cc_final: 0.8697 (m-40)
REVERT: D   37 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8946 (tt)
REVERT: E   22 ARG cc_start: 0.7846 (ttt-90) cc_final: 0.7462 (tpt-90)
REVERT: E   67 SER cc_start: 0.8944 (t) cc_final: 0.8602 (p)
REVERT: F   28 TYR cc_start: 0.6653 (OUTLIER) cc_final: 0.6383 (m-80)
  outliers start: 28
  outliers final: 18
  residues processed: 269
  average time/residue: 0.1958
  time to fit residues: 67.9505
Evaluate side-chains
  262 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 240
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   61 SER
Chi-restraints excluded: chain A residue   67 TYR
Chi-restraints excluded: chain A residue   87 GLU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  165 GLU
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain B residue   14 MET
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  198 LYS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   48 MET
Chi-restraints excluded: chain E residue   15 LEU
Chi-restraints excluded: chain F residue   28 TYR
Chi-restraints excluded: chain F residue   57 MET
Chi-restraints excluded: chain G residue   53 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 62 optimal weight:    0.1980
   chunk 72 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 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 = 0.3680 r_free = 0.3680 target = 0.122747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.096838 restraints weight = 13268.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.099377 restraints weight = 8148.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.101131 restraints weight = 5873.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.3110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6710  Z= 0.215
  Angle     :  0.752  12.027   9034  Z= 0.377
  Chirality :  0.041   0.187   1012
  Planarity :  0.004   0.043   1122
  Dihedral  :  4.417  19.054    888
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 22.82 %
    Favored  : 73.52 %
  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:  0.59 (0.30), residues: 808
  helix:  1.47 (0.21), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.78 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.101   0.002   TRP G  30 
 HIS   0.003   0.001   HIS D  77 
 PHE   0.022   0.002   PHE D  61 
 TYR   0.018   0.001   TYR B 205 
 ARG   0.007   0.001   ARG E  21 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 267
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LYS cc_start: 0.8295 (tttt) cc_final: 0.8008 (mtpt)
REVERT: A   41 VAL cc_start: 0.8757 (m) cc_final: 0.8554 (p)
REVERT: B   14 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8378 (tpt)
REVERT: B   78 TYR cc_start: 0.7180 (t80) cc_final: 0.6670 (t80)
REVERT: B  129 MET cc_start: 0.8047 (tpp) cc_final: 0.7841 (tpp)
REVERT: B  215 VAL cc_start: 0.9134 (m) cc_final: 0.8889 (p)
REVERT: C   12 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7171 (tm-30)
REVERT: C   13 MET cc_start: 0.7502 (ptp) cc_final: 0.7112 (ptp)
REVERT: D   37 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8951 (tt)
REVERT: E   22 ARG cc_start: 0.7829 (ttt-90) cc_final: 0.7543 (tpt-90)
REVERT: E   30 TRP cc_start: 0.8799 (m100) cc_final: 0.8477 (m100)
REVERT: E   67 SER cc_start: 0.8939 (t) cc_final: 0.8599 (p)
REVERT: F   28 TYR cc_start: 0.6544 (OUTLIER) cc_final: 0.6334 (m-80)
  outliers start: 26
  outliers final: 17
  residues processed: 279
  average time/residue: 0.1959
  time to fit residues: 70.4358
Evaluate side-chains
  265 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 245
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   61 SER
Chi-restraints excluded: chain A residue   87 GLU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain B residue   14 MET
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   48 MET
Chi-restraints excluded: chain E residue   15 LEU
Chi-restraints excluded: chain F residue   28 TYR
Chi-restraints excluded: chain F residue   57 MET
Chi-restraints excluded: chain G residue   53 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 67 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 65 optimal weight:   10.0000
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 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 = 0.3694 r_free = 0.3694 target = 0.123575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.097806 restraints weight = 13251.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.100319 restraints weight = 8147.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.102096 restraints weight = 5871.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6710  Z= 0.222
  Angle     :  0.785  13.054   9034  Z= 0.389
  Chirality :  0.042   0.213   1012
  Planarity :  0.004   0.041   1122
  Dihedral  :  4.396  18.992    888
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 25.49 %
    Favored  : 71.83 %
  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:  0.53 (0.30), residues: 808
  helix:  1.41 (0.21), residues: 593
  sheet:  None (None), residues: 0
  loop : -2.76 (0.40), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.077   0.002   TRP G  30 
 HIS   0.002   0.000   HIS D  77 
 PHE   0.022   0.002   PHE D  61 
 TYR   0.018   0.002   TYR B  19 
 ARG   0.007   0.001   ARG E  21 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 251
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LYS cc_start: 0.8251 (tttt) cc_final: 0.7956 (mtpt)
REVERT: A  145 ASP cc_start: 0.7370 (t0) cc_final: 0.7125 (t0)
REVERT: B   78 TYR cc_start: 0.7137 (t80) cc_final: 0.6706 (t80)
REVERT: B  215 VAL cc_start: 0.9107 (m) cc_final: 0.8889 (p)
REVERT: C   12 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7185 (tm-30)
REVERT: C   13 MET cc_start: 0.7479 (ptp) cc_final: 0.7099 (ptp)
REVERT: D   37 LEU cc_start: 0.9207 (tt) cc_final: 0.8975 (tt)
REVERT: E   22 ARG cc_start: 0.7769 (ttt-90) cc_final: 0.7485 (tpt-90)
REVERT: E   30 TRP cc_start: 0.8712 (m100) cc_final: 0.8414 (m100)
REVERT: E   67 SER cc_start: 0.8886 (t) cc_final: 0.8563 (p)
REVERT: F   28 TYR cc_start: 0.6517 (OUTLIER) cc_final: 0.6301 (m-80)
  outliers start: 19
  outliers final: 16
  residues processed: 262
  average time/residue: 0.1922
  time to fit residues: 64.9304
Evaluate side-chains
  256 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 239
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   61 SER
Chi-restraints excluded: chain A residue   67 TYR
Chi-restraints excluded: chain A residue   87 GLU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain D residue   48 MET
Chi-restraints excluded: chain E residue   15 LEU
Chi-restraints excluded: chain F residue   28 TYR
Chi-restraints excluded: chain F residue   57 MET
Chi-restraints excluded: chain G residue   53 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 50 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 71 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 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 = 0.3656 r_free = 0.3656 target = 0.120873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.095712 restraints weight = 13442.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.098095 restraints weight = 8366.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.099657 restraints weight = 6070.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.3282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   6710  Z= 0.284
  Angle     :  0.832  15.100   9034  Z= 0.414
  Chirality :  0.043   0.218   1012
  Planarity :  0.004   0.046   1122
  Dihedral  :  4.556  20.349    888
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 25.77 %
    Favored  : 71.13 %
  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:  0.43 (0.29), residues: 808
  helix:  1.33 (0.21), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.78 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.077   0.002   TRP G  30 
 HIS   0.003   0.001   HIS D  77 
 PHE   0.026   0.002   PHE D  61 
 TYR   0.030   0.002   TYR A  19 
 ARG   0.008   0.001   ARG G  21 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 240
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  129 MET cc_start: 0.8067 (tpp) cc_final: 0.7790 (tpp)
REVERT: C   12 GLU cc_start: 0.7385 (tm-30) cc_final: 0.7146 (tm-30)
REVERT: C   13 MET cc_start: 0.7408 (ptp) cc_final: 0.7039 (ptp)
REVERT: E    8 LYS cc_start: 0.7022 (mmtm) cc_final: 0.6770 (mptt)
REVERT: E   22 ARG cc_start: 0.7820 (ttt-90) cc_final: 0.7554 (tpt-90)
REVERT: E   57 MET cc_start: 0.8723 (mtt) cc_final: 0.8495 (mtt)
REVERT: E   67 SER cc_start: 0.8964 (t) cc_final: 0.8600 (p)
REVERT: F   28 TYR cc_start: 0.6628 (OUTLIER) cc_final: 0.6419 (m-80)
REVERT: F   74 MET cc_start: 0.7318 (ttt) cc_final: 0.6550 (tpp)
REVERT: G   30 TRP cc_start: 0.8553 (m-90) cc_final: 0.8240 (m-90)
  outliers start: 22
  outliers final: 18
  residues processed: 252
  average time/residue: 0.1970
  time to fit residues: 63.3592
Evaluate side-chains
  254 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 235
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   61 SER
Chi-restraints excluded: chain A residue   67 TYR
Chi-restraints excluded: chain A residue   87 GLU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  165 GLU
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain E residue   15 LEU
Chi-restraints excluded: chain F residue   28 TYR
Chi-restraints excluded: chain F residue   57 MET
Chi-restraints excluded: chain G residue   53 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 63 optimal weight:    0.0370
   chunk 66 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 74 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.7258

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 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 = 0.3703 r_free = 0.3703 target = 0.123916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.097799 restraints weight = 13586.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.100320 restraints weight = 8344.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.102124 restraints weight = 6051.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6710  Z= 0.225
  Angle     :  0.844  15.949   9034  Z= 0.412
  Chirality :  0.042   0.247   1012
  Planarity :  0.004   0.046   1122
  Dihedral  :  4.475  19.232    888
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 25.63 %
    Favored  : 71.41 %
  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:  0.40 (0.29), residues: 808
  helix:  1.28 (0.21), residues: 594
  sheet:  None (None), residues: 0
  loop : -2.71 (0.40), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.073   0.002   TRP G  30 
 HIS   0.002   0.000   HIS D  77 
 PHE   0.022   0.001   PHE D  61 
 TYR   0.017   0.001   TYR B  19 
 ARG   0.009   0.001   ARG B 148 

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

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

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1616 Ramachandran restraints generated.
    808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 257
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 ASP cc_start: 0.7272 (t0) cc_final: 0.7054 (t0)
REVERT: C   12 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7195 (tm-30)
REVERT: C   13 MET cc_start: 0.7413 (ptp) cc_final: 0.7072 (ptp)
REVERT: E   22 ARG cc_start: 0.7906 (ttt-90) cc_final: 0.7512 (tpt-90)
REVERT: E   30 TRP cc_start: 0.8567 (m100) cc_final: 0.8223 (m100)
REVERT: E   67 SER cc_start: 0.8934 (t) cc_final: 0.8553 (p)
REVERT: F   74 MET cc_start: 0.7371 (ttt) cc_final: 0.6555 (tpp)
REVERT: G   30 TRP cc_start: 0.8322 (m-90) cc_final: 0.7836 (m100)
REVERT: G   70 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7809 (tm-30)
  outliers start: 21
  outliers final: 16
  residues processed: 267
  average time/residue: 0.1968
  time to fit residues: 68.0567
Evaluate side-chains
  259 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 243
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   67 TYR
Chi-restraints excluded: chain A residue   87 GLU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   80 ARG
Chi-restraints excluded: chain B residue  186 ASN
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain E residue   15 LEU
Chi-restraints excluded: chain F residue   57 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   chunk 74 optimal weight:    8.9990
   chunk 52 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  25 ASN ** 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 = 0.3707 r_free = 0.3707 target = 0.124348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.098168 restraints weight = 13617.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.100714 restraints weight = 8403.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.102457 restraints weight = 6087.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.3612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   6710  Z= 0.233
  Angle     :  0.844  16.797   9034  Z= 0.413
  Chirality :  0.042   0.257   1012
  Planarity :  0.004   0.047   1122
  Dihedral  :  4.451  18.829    888
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 26.62 %
    Favored  : 70.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.43 (0.29), residues: 808
  helix:  1.27 (0.21), residues: 590
  sheet:  None (None), residues: 0
  loop : -2.54 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.069   0.002   TRP G  30 
 HIS   0.002   0.001   HIS F  45 
 PHE   0.022   0.002   PHE D  61 
 TYR   0.017   0.001   TYR D  28 
 ARG   0.008   0.001   ARG G  21 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2327.81 seconds
wall clock time: 42 minutes 31.35 seconds (2551.35 seconds total)