Starting phenix.real_space_refine
on Tue Mar  3 18:18:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sat_24956/03_2026/7sat_24956.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sat_24956/03_2026/7sat_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sat_24956/03_2026/7sat_24956.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sat_24956/03_2026/7sat_24956.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sat_24956/03_2026/7sat_24956.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sat_24956/03_2026/7sat_24956.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.48, per 1000 atoms: 0.22
  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: 0.61
  Conformation dependent library (CDL) restraints added in 213.6 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: 0.16
  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: 0.81

  Time building geometry restraints manager: 0.75 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:             0.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.250
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.370
-------------------------------------------------------------------------------
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= 0.173
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (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
 ARG   0.009   0.001   ARG D  21 
 TYR   0.025   0.002   TYR D   7 
 PHE   0.019   0.001   PHE D  61 
 TRP   0.094   0.003   TRP G  30 
 HIS   0.009   0.001   HIS C  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 6710)
  covalent geometry    : angle       0.75503 ( 9034)
  hydrogen bonds       : bond        0.13191 (  441)
  hydrogen bonds       : angle       5.68134 ( 1314)

*********************** 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  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 ASP cc_start: 0.8055 (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: 0.8459 (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: 0.6969 (ptt) cc_final: 0.6593 (ptt)
REVERT: G   51 GLU cc_start: 0.8388 (mp0) cc_final: 0.8174 (mp0)
  outliers start: 2
  outliers final: 0
  residues processed: 281
  average time/residue: 0.0774
  time to fit residues: 28.5016
Evaluate side-chains
  234 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0050
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.5994

-------------------------------------------------------------------------------
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 = 0.3677 r_free = 0.3677 target = 0.121605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.096349 restraints weight = 13442.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.098986 restraints weight = 8053.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.100859 restraints weight = 5739.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.101914 restraints weight = 4582.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.102793 restraints weight = 3988.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.1956

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= 0.137
  Angle     :  0.702  11.909   9034  Z= 0.356
  Chirality :  0.039   0.151   1012
  Planarity :  0.004   0.056   1122
  Dihedral  :  4.542  19.973    888
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.94 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.30), residues: 808
  helix:  1.27 (0.21), residues: 595
  sheet:  None (None), residues: 0
  loop : -2.82 (0.42), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  80 
 TYR   0.017   0.002   TYR B 205 
 PHE   0.021   0.002   PHE D  54 
 TRP   0.062   0.002   TRP G  30 
 HIS   0.005   0.001   HIS C  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6710)
  covalent geometry    : angle       0.70229 ( 9034)
  hydrogen bonds       : bond        0.03914 (  441)
  hydrogen bonds       : angle       4.33742 ( 1314)

*********************** 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
  278 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 261
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 ARG cc_start: 0.8731 (mmt-90) cc_final: 0.7787 (tpp-160)
REVERT: B   78 TYR cc_start: 0.6796 (t80) cc_final: 0.6576 (t80)
REVERT: B  155 MET cc_start: 0.1468 (mmt) cc_final: 0.0780 (mmt)
REVERT: C   12 GLU cc_start: 0.7366 (tm-30) cc_final: 0.7162 (tm-30)
REVERT: C   13 MET cc_start: 0.7458 (ptp) cc_final: 0.7079 (ptp)
REVERT: C   24 LEU cc_start: 0.9041 (mt) cc_final: 0.8395 (tp)
REVERT: C   60 GLU cc_start: 0.8459 (pp20) cc_final: 0.7963 (pp20)
REVERT: D   48 MET cc_start: 0.6886 (ptt) cc_final: 0.6669 (ptt)
REVERT: E   17 SER cc_start: 0.7230 (m) cc_final: 0.6935 (p)
REVERT: E   22 ARG cc_start: 0.7878 (ttt-90) cc_final: 0.7641 (tpt-90)
REVERT: G   14 TYR cc_start: 0.7821 (t80) cc_final: 0.7613 (t80)
REVERT: G   30 TRP cc_start: 0.8392 (m-90) cc_final: 0.8062 (m-90)
  outliers start: 17
  outliers final: 13
  residues processed: 268
  average time/residue: 0.0812
  time to fit residues: 28.5821
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  : 0.243 
-------------------------------------------------------------------------------
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 68 optimal weight:    2.9990
   chunk 32 optimal weight:    8.9990
   chunk 45 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 66 optimal weight:    9.9990
   chunk 8 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.118704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.093078 restraints weight = 13393.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.095562 restraints weight = 8179.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.097293 restraints weight = 5890.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.098316 restraints weight = 4755.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.099037 restraints weight = 4172.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6710  Z= 0.164
  Angle     :  0.712  11.323   9034  Z= 0.355
  Chirality :  0.040   0.147   1012
  Planarity :  0.004   0.054   1122
  Dihedral  :  4.493  19.444    888
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 15.63 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.30), residues: 808
  helix:  1.40 (0.21), residues: 589
  sheet:  None (None), residues: 0
  loop : -2.95 (0.40), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  21 
 TYR   0.019   0.002   TYR A  78 
 PHE   0.023   0.002   PHE D  61 
 TRP   0.042   0.002   TRP G  30 
 HIS   0.003   0.001   HIS E  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6710)
  covalent geometry    : angle       0.71168 ( 9034)
  hydrogen bonds       : bond        0.03693 (  441)
  hydrogen bonds       : angle       4.29314 ( 1314)

*********************** 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
  280 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 250
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASN cc_start: 0.8864 (p0) cc_final: 0.8557 (p0)
REVERT: A  118 ARG cc_start: 0.8280 (ppt170) cc_final: 0.7961 (ppt170)
REVERT: A  204 ARG cc_start: 0.8833 (mmt-90) cc_final: 0.7886 (tpp-160)
REVERT: B   78 TYR cc_start: 0.6831 (t80) cc_final: 0.6570 (t80)
REVERT: B   80 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7520 (ptt90)
REVERT: B  155 MET cc_start: 0.1262 (mmt) cc_final: 0.0882 (mmt)
REVERT: C   12 GLU cc_start: 0.7366 (tm-30) cc_final: 0.7091 (tm-30)
REVERT: C   13 MET cc_start: 0.7472 (ptp) cc_final: 0.7071 (ptp)
REVERT: C   60 GLU cc_start: 0.8480 (pp20) cc_final: 0.8039 (pp20)
REVERT: D   37 LEU cc_start: 0.9222 (tt) cc_final: 0.8990 (tt)
REVERT: E   22 ARG cc_start: 0.7872 (ttt-90) cc_final: 0.7599 (tpt-90)
REVERT: F   70 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7420 (pm20)
  outliers start: 30
  outliers final: 22
  residues processed: 264
  average time/residue: 0.0829
  time to fit residues: 28.5949
Evaluate side-chains
  251 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 227
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
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   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  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   63 LEU
Chi-restraints excluded: chain B residue   80 ARG
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   76 TYR
Chi-restraints excluded: chain D residue   35 VAL
Chi-restraints excluded: chain F residue   57 MET
Chi-restraints excluded: chain F residue   70 GLU
Chi-restraints excluded: chain G residue   52 MET
Chi-restraints excluded: chain G residue   53 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    8.9990
   chunk 27 optimal weight:    0.0070
   chunk 26 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.9602

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

Flipped N/Q/H residues before XYZ refinement:
** B  12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.120812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.095020 restraints weight = 13537.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.097485 restraints weight = 8283.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.099324 restraints weight = 5981.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.100499 restraints weight = 4803.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.101190 restraints weight = 4156.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6710  Z= 0.134
  Angle     :  0.704  12.281   9034  Z= 0.349
  Chirality :  0.039   0.170   1012
  Planarity :  0.004   0.050   1122
  Dihedral  :  4.398  19.468    888
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.56 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.30), residues: 808
  helix:  1.38 (0.21), residues: 590
  sheet:  None (None), residues: 0
  loop : -2.91 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  21 
 TYR   0.026   0.002   TYR C   4 
 PHE   0.020   0.001   PHE E  61 
 TRP   0.055   0.002   TRP G  30 
 HIS   0.003   0.000   HIS D  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6710)
  covalent geometry    : angle       0.70423 ( 9034)
  hydrogen bonds       : bond        0.03531 (  441)
  hydrogen bonds       : angle       4.19146 ( 1314)

*********************** 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: 27
    poor density    : 258
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 VAL cc_start: 0.8603 (m) cc_final: 0.7959 (t)
REVERT: A  118 ARG cc_start: 0.8211 (ppt170) cc_final: 0.7972 (ppt170)
REVERT: A  194 THR cc_start: 0.8536 (m) cc_final: 0.8210 (m)
REVERT: B   80 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7533 (ptt90)
REVERT: B  155 MET cc_start: 0.1160 (mmt) cc_final: 0.0954 (mmt)
REVERT: C   12 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7070 (tm-30)
REVERT: C   13 MET cc_start: 0.7416 (ptp) cc_final: 0.7039 (ptp)
REVERT: C   25 ASN cc_start: 0.9087 (t0) cc_final: 0.8849 (m-40)
REVERT: C   60 GLU cc_start: 0.8342 (pp20) cc_final: 0.7959 (pp20)
REVERT: D   37 LEU cc_start: 0.9162 (tt) cc_final: 0.8832 (tt)
REVERT: E   17 SER cc_start: 0.7102 (m) cc_final: 0.6852 (p)
REVERT: E   22 ARG cc_start: 0.7911 (ttt-90) cc_final: 0.7598 (tpt-90)
REVERT: E   67 SER cc_start: 0.8888 (t) cc_final: 0.8574 (p)
REVERT: F   28 TYR cc_start: 0.6896 (OUTLIER) cc_final: 0.6449 (m-80)
REVERT: F   37 LEU cc_start: 0.9017 (tp) cc_final: 0.8505 (tp)
REVERT: G   30 TRP cc_start: 0.8621 (m-90) cc_final: 0.8363 (m-90)
  outliers start: 27
  outliers final: 17
  residues processed: 271
  average time/residue: 0.0849
  time to fit residues: 30.0626
Evaluate side-chains
  251 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 232
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
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 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 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0470
   chunk 2 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 60 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 38 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.7078

-------------------------------------------------------------------------------
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 = 0.3684 r_free = 0.3684 target = 0.122477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.096546 restraints weight = 13756.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.099103 restraints weight = 8422.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.100892 restraints weight = 6044.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.102147 restraints weight = 4856.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.102695 restraints weight = 4194.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6710  Z= 0.131
  Angle     :  0.708  12.152   9034  Z= 0.354
  Chirality :  0.040   0.170   1012
  Planarity :  0.004   0.048   1122
  Dihedral  :  4.336  19.350    888
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 21.69 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.30), residues: 808
  helix:  1.46 (0.21), residues: 590
  sheet:  None (None), residues: 0
  loop : -2.86 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  21 
 TYR   0.032   0.002   TYR B  78 
 PHE   0.020   0.002   PHE D  61 
 TRP   0.036   0.001   TRP G  30 
 HIS   0.003   0.000   HIS D  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6710)
  covalent geometry    : angle       0.70750 ( 9034)
  hydrogen bonds       : bond        0.03547 (  441)
  hydrogen bonds       : angle       4.07259 ( 1314)

*********************** 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
  287 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 258
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LYS cc_start: 0.8206 (tttt) cc_final: 0.7944 (mtpt)
REVERT: A  204 ARG cc_start: 0.8609 (mmt-90) cc_final: 0.7497 (tpp-160)
REVERT: B   78 TYR cc_start: 0.7047 (t80) cc_final: 0.6414 (t80)
REVERT: B  129 MET cc_start: 0.8021 (tpp) cc_final: 0.7788 (tpp)
REVERT: C   12 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7104 (tm-30)
REVERT: C   13 MET cc_start: 0.7464 (ptp) cc_final: 0.7065 (ptp)
REVERT: C   25 ASN cc_start: 0.9010 (t0) cc_final: 0.8791 (m-40)
REVERT: C   60 GLU cc_start: 0.8219 (pp20) cc_final: 0.7871 (pp20)
REVERT: D   37 LEU cc_start: 0.9121 (tt) cc_final: 0.8843 (tt)
REVERT: E   17 SER cc_start: 0.7092 (m) cc_final: 0.6858 (p)
REVERT: E   22 ARG cc_start: 0.7887 (ttt-90) cc_final: 0.7605 (tpt-90)
REVERT: E   30 TRP cc_start: 0.8725 (m100) cc_final: 0.8483 (m100)
REVERT: E   67 SER cc_start: 0.8870 (t) cc_final: 0.8563 (p)
REVERT: F   25 ASN cc_start: 0.8782 (t0) cc_final: 0.8562 (t0)
REVERT: F   37 LEU cc_start: 0.8936 (tp) cc_final: 0.8696 (tp)
REVERT: G   21 ARG cc_start: 0.8875 (mtp85) cc_final: 0.8655 (mtm180)
REVERT: G   70 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7875 (tm-30)
  outliers start: 29
  outliers final: 21
  residues processed: 273
  average time/residue: 0.0837
  time to fit residues: 29.6750
Evaluate side-chains
  267 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 246
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
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  193 ILE
Chi-restraints excluded: chain B residue    6 ASN
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   58 LEU
Chi-restraints excluded: chain B residue   63 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   48 MET
Chi-restraints excluded: chain E residue   15 LEU
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 2 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B   6 ASN
** B 166 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 = 0.3668 r_free = 0.3668 target = 0.121504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.095631 restraints weight = 13575.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.098213 restraints weight = 8334.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.099939 restraints weight = 6012.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.101161 restraints weight = 4850.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.101602 restraints weight = 4206.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6710  Z= 0.140
  Angle     :  0.712  12.568   9034  Z= 0.357
  Chirality :  0.040   0.160   1012
  Planarity :  0.004   0.047   1122
  Dihedral  :  4.370  19.172    888
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 22.54 %
    Favored  : 73.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.30), residues: 808
  helix:  1.41 (0.21), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.79 (0.40), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  21 
 TYR   0.022   0.001   TYR B  78 
 PHE   0.020   0.002   PHE D  61 
 TRP   0.064   0.002   TRP G  30 
 HIS   0.003   0.001   HIS D  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6710)
  covalent geometry    : angle       0.71191 ( 9034)
  hydrogen bonds       : bond        0.03518 (  441)
  hydrogen bonds       : angle       4.14286 ( 1314)

*********************** 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
  285 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 258
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 ARG cc_start: 0.8642 (mmt-90) cc_final: 0.7614 (tpp-160)
REVERT: B   14 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8404 (tpt)
REVERT: B  215 VAL cc_start: 0.9140 (m) cc_final: 0.8886 (p)
REVERT: C   12 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7112 (tm-30)
REVERT: C   13 MET cc_start: 0.7440 (ptp) cc_final: 0.7038 (ptp)
REVERT: C   25 ASN cc_start: 0.9023 (t0) cc_final: 0.8770 (m-40)
REVERT: C   60 GLU cc_start: 0.8169 (pp20) cc_final: 0.7859 (pp20)
REVERT: D   37 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8882 (tt)
REVERT: E   22 ARG cc_start: 0.7889 (ttt-90) cc_final: 0.7561 (tpt-90)
REVERT: E   67 SER cc_start: 0.8878 (t) cc_final: 0.8574 (p)
REVERT: G   21 ARG cc_start: 0.8961 (mtp85) cc_final: 0.8719 (mtp85)
  outliers start: 27
  outliers final: 20
  residues processed: 271
  average time/residue: 0.0788
  time to fit residues: 28.1423
Evaluate side-chains
  264 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 242
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
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   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  127 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   58 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   15 LEU
Chi-restraints excluded: chain F residue   57 MET
Chi-restraints excluded: chain F residue   70 GLU
Chi-restraints excluded: chain G residue   19 LYS
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:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 7 optimal weight:    0.7980
   chunk 64 optimal weight:    7.9990
   chunk 56 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 4 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   chunk 42 optimal weight:    9.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
B   6 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 = 0.3649 r_free = 0.3649 target = 0.120140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.093899 restraints weight = 13799.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.096289 restraints weight = 8518.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.098097 restraints weight = 6249.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.099297 restraints weight = 5071.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.099843 restraints weight = 4417.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6710  Z= 0.160
  Angle     :  0.756  12.425   9034  Z= 0.376
  Chirality :  0.042   0.187   1012
  Planarity :  0.004   0.048   1122
  Dihedral  :  4.426  19.426    888
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 22.39 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.30), residues: 808
  helix:  1.41 (0.21), residues: 593
  sheet:  None (None), residues: 0
  loop : -2.82 (0.39), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  21 
 TYR   0.019   0.001   TYR A  78 
 PHE   0.022   0.002   PHE D  61 
 TRP   0.048   0.002   TRP G  30 
 HIS   0.003   0.001   HIS D  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 6710)
  covalent geometry    : angle       0.75576 ( 9034)
  hydrogen bonds       : bond        0.03608 (  441)
  hydrogen bonds       : angle       4.21883 ( 1314)

*********************** 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
  279 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 246
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LYS cc_start: 0.8301 (tttt) cc_final: 0.8002 (mtpt)
REVERT: A  204 ARG cc_start: 0.8679 (mmt-90) cc_final: 0.7730 (tpp-160)
REVERT: B   14 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8477 (tpt)
REVERT: B   78 TYR cc_start: 0.7115 (t80) cc_final: 0.6563 (t80)
REVERT: B  215 VAL cc_start: 0.9154 (m) cc_final: 0.8908 (p)
REVERT: C   12 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7122 (tm-30)
REVERT: C   13 MET cc_start: 0.7453 (ptp) cc_final: 0.7053 (ptp)
REVERT: C   25 ASN cc_start: 0.9029 (t0) cc_final: 0.8818 (m-40)
REVERT: C   60 GLU cc_start: 0.8167 (pp20) cc_final: 0.7915 (pp20)
REVERT: D   37 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8911 (tt)
REVERT: E   22 ARG cc_start: 0.7881 (ttt-90) cc_final: 0.7583 (tpt-90)
REVERT: E   30 TRP cc_start: 0.8741 (m100) cc_final: 0.8470 (m100)
REVERT: E   67 SER cc_start: 0.8943 (t) cc_final: 0.8595 (p)
REVERT: G   21 ARG cc_start: 0.9005 (mtp85) cc_final: 0.8799 (mtp85)
  outliers start: 33
  outliers final: 27
  residues processed: 266
  average time/residue: 0.0833
  time to fit residues: 29.0189
Evaluate side-chains
  263 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 234
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
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   67 TYR
Chi-restraints excluded: chain A residue   87 GLU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain B residue    6 ASN
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   58 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   53 LEU
Chi-restraints excluded: chain C residue   76 TYR
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   15 LEU
Chi-restraints excluded: chain F residue   57 MET
Chi-restraints excluded: chain F residue   70 GLU
Chi-restraints excluded: chain G residue   19 LYS
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 76 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 29 optimal weight:    0.4980
   chunk 4 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 32 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9990
   chunk 27 optimal weight:   20.0000
   chunk 77 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    1.4988

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

Flipped N/Q/H residues before XYZ refinement:
B  12 GLN
** B 166 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 = 0.3650 r_free = 0.3650 target = 0.120288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.094122 restraints weight = 13706.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.096605 restraints weight = 8465.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.098416 restraints weight = 6149.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.099625 restraints weight = 4959.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.100120 restraints weight = 4301.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.3067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6710  Z= 0.162
  Angle     :  0.790  15.746   9034  Z= 0.392
  Chirality :  0.043   0.194   1012
  Planarity :  0.004   0.047   1122
  Dihedral  :  4.461  19.594    888
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 22.82 %
    Favored  : 73.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.30), residues: 808
  helix:  1.36 (0.21), residues: 593
  sheet:  None (None), residues: 0
  loop : -2.85 (0.39), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  80 
 TYR   0.016   0.001   TYR B  78 
 PHE   0.022   0.002   PHE D  61 
 TRP   0.095   0.002   TRP G  30 
 HIS   0.003   0.001   HIS D  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6710)
  covalent geometry    : angle       0.79024 ( 9034)
  hydrogen bonds       : bond        0.03700 (  441)
  hydrogen bonds       : angle       4.27905 ( 1314)

*********************** 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
  272 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 243
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 ARG cc_start: 0.8668 (mmt-90) cc_final: 0.7762 (tpp-160)
REVERT: B   14 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8427 (tpt)
REVERT: B   78 TYR cc_start: 0.7039 (t80) cc_final: 0.6513 (t80)
REVERT: B  129 MET cc_start: 0.8074 (tpp) cc_final: 0.7771 (tpp)
REVERT: B  215 VAL cc_start: 0.9185 (m) cc_final: 0.8981 (p)
REVERT: C   12 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7119 (tm-30)
REVERT: C   13 MET cc_start: 0.7418 (ptp) cc_final: 0.7051 (ptp)
REVERT: C   25 ASN cc_start: 0.8986 (t0) cc_final: 0.8766 (m-40)
REVERT: C   60 GLU cc_start: 0.8178 (pp20) cc_final: 0.7964 (pp20)
REVERT: D   37 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8931 (tt)
REVERT: E   22 ARG cc_start: 0.7854 (ttt-90) cc_final: 0.7607 (tpt-90)
REVERT: E   30 TRP cc_start: 0.8752 (m100) cc_final: 0.8548 (m100)
REVERT: E   67 SER cc_start: 0.8931 (t) cc_final: 0.8582 (p)
REVERT: G   70 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7815 (tm-30)
  outliers start: 29
  outliers final: 23
  residues processed: 261
  average time/residue: 0.0761
  time to fit residues: 26.3161
Evaluate side-chains
  257 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 232
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
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   67 TYR
Chi-restraints excluded: chain A residue   87 GLU
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  127 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   58 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   76 TYR
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   15 LEU
Chi-restraints excluded: chain F residue   57 MET
Chi-restraints excluded: chain F residue   70 GLU
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 68 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 58 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0870
   chunk 12 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.6558

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.122644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.096366 restraints weight = 13780.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.098925 restraints weight = 8474.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.100701 restraints weight = 6135.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.101765 restraints weight = 4962.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.102657 restraints weight = 4360.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6710  Z= 0.144
  Angle     :  0.820  16.509   9034  Z= 0.401
  Chirality :  0.041   0.239   1012
  Planarity :  0.004   0.045   1122
  Dihedral  :  4.461  20.792    888
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 24.51 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.30), residues: 808
  helix:  1.26 (0.21), residues: 598
  sheet:  None (None), residues: 0
  loop : -2.69 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  21 
 TYR   0.022   0.001   TYR G  14 
 PHE   0.022   0.001   PHE D  61 
 TRP   0.117   0.003   TRP G  30 
 HIS   0.002   0.000   HIS F  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6710)
  covalent geometry    : angle       0.82001 ( 9034)
  hydrogen bonds       : bond        0.03811 (  441)
  hydrogen bonds       : angle       4.27997 ( 1314)

*********************** 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
  277 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 253
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 LYS cc_start: 0.8238 (tttt) cc_final: 0.7964 (mtpt)
REVERT: A  204 ARG cc_start: 0.8628 (mmt-90) cc_final: 0.7756 (tpp-160)
REVERT: B   14 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8369 (tpt)
REVERT: B   78 TYR cc_start: 0.7041 (t80) cc_final: 0.6551 (t80)
REVERT: B  129 MET cc_start: 0.8030 (tpp) cc_final: 0.7712 (tpp)
REVERT: B  215 VAL cc_start: 0.9165 (m) cc_final: 0.8932 (p)
REVERT: C   12 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7142 (tm-30)
REVERT: C   13 MET cc_start: 0.7440 (ptp) cc_final: 0.7052 (ptp)
REVERT: C   25 ASN cc_start: 0.8868 (t0) cc_final: 0.8627 (m-40)
REVERT: D   37 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8916 (tt)
REVERT: E   22 ARG cc_start: 0.7824 (ttt-90) cc_final: 0.7591 (tpt-90)
REVERT: E   67 SER cc_start: 0.8850 (t) cc_final: 0.8539 (p)
REVERT: G   30 TRP cc_start: 0.8262 (m-90) cc_final: 0.7867 (m100)
REVERT: G   70 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7752 (tm-30)
  outliers start: 24
  outliers final: 19
  residues processed: 265
  average time/residue: 0.0799
  time to fit residues: 27.8753
Evaluate side-chains
  257 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 236
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
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   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   14 MET
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   34 VAL
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   63 LEU
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 E residue   15 LEU
Chi-restraints excluded: chain F residue   57 MET
Chi-restraints excluded: chain F residue   70 GLU
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 38 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 76 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3699 r_free = 0.3699 target = 0.123471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.097291 restraints weight = 13788.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.099858 restraints weight = 8502.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.101655 restraints weight = 6166.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.102657 restraints weight = 4983.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.102657 restraints weight = 4377.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.3448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6710  Z= 0.151
  Angle     :  0.851  17.364   9034  Z= 0.416
  Chirality :  0.042   0.250   1012
  Planarity :  0.004   0.045   1122
  Dihedral  :  4.480  19.461    888
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 13.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 25.77 %
    Favored  : 70.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.30), residues: 808
  helix:  1.27 (0.21), residues: 589
  sheet:  None (None), residues: 0
  loop : -2.63 (0.40), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 148 
 TYR   0.016   0.001   TYR B  78 
 PHE   0.022   0.002   PHE D  61 
 TRP   0.105   0.002   TRP G  30 
 HIS   0.002   0.000   HIS F  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 6710)
  covalent geometry    : angle       0.85055 ( 9034)
  hydrogen bonds       : bond        0.03928 (  441)
  hydrogen bonds       : angle       4.30720 ( 1314)

********************** 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
  271 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 248
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 LYS cc_start: 0.8193 (tttt) cc_final: 0.7954 (mtpt)
REVERT: A  204 ARG cc_start: 0.8644 (mmt-90) cc_final: 0.7769 (tpp-160)
REVERT: B   78 TYR cc_start: 0.7028 (t80) cc_final: 0.6551 (t80)
REVERT: B  129 MET cc_start: 0.8047 (tpp) cc_final: 0.7734 (tpp)
REVERT: B  215 VAL cc_start: 0.9156 (m) cc_final: 0.8943 (p)
REVERT: C   12 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7161 (tm-30)
REVERT: C   13 MET cc_start: 0.7527 (ptp) cc_final: 0.7105 (ptp)
REVERT: C   25 ASN cc_start: 0.8803 (t0) cc_final: 0.8525 (m-40)
REVERT: D   37 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8952 (tt)
REVERT: E   22 ARG cc_start: 0.7770 (ttt-90) cc_final: 0.7562 (tpt-90)
REVERT: E   30 TRP cc_start: 0.8569 (m100) cc_final: 0.8256 (m100)
REVERT: E   67 SER cc_start: 0.8874 (t) cc_final: 0.8318 (p)
REVERT: G   30 TRP cc_start: 0.8104 (m-90) cc_final: 0.7884 (m100)
REVERT: G   70 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7612 (tm-30)
  outliers start: 23
  outliers final: 20
  residues processed: 260
  average time/residue: 0.0852
  time to fit residues: 28.8040
Evaluate side-chains
  261 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 240
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
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  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   58 LEU
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   15 LEU
Chi-restraints excluded: chain F residue   70 GLU
Chi-restraints excluded: chain G residue   53 LEU
Chi-restraints excluded: chain G residue   76 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0970
   chunk 26 optimal weight:    0.0870
   chunk 68 optimal weight:    0.1980
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 73 optimal weight:    0.4980
   overall best weight:    0.3356

-------------------------------------------------------------------------------
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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3742 r_free = 0.3742 target = 0.126747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.101136 restraints weight = 13499.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.103794 restraints weight = 8260.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.105610 restraints weight = 5916.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.106694 restraints weight = 4756.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.107640 restraints weight = 4156.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.3669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6710  Z= 0.151
  Angle     :  0.869  16.736   9034  Z= 0.419
  Chirality :  0.042   0.207   1012
  Planarity :  0.004   0.046   1122
  Dihedral  :  4.447  18.826    888
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 26.48 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.30), residues: 808
  helix:  1.23 (0.21), residues: 590
  sheet:  None (None), residues: 0
  loop : -2.57 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E   6 
 TYR   0.023   0.001   TYR G  14 
 PHE   0.026   0.001   PHE D  61 
 TRP   0.095   0.002   TRP G  30 
 HIS   0.002   0.000   HIS D  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 6710)
  covalent geometry    : angle       0.86897 ( 9034)
  hydrogen bonds       : bond        0.03950 (  441)
  hydrogen bonds       : angle       4.28069 ( 1314)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1215.23 seconds
wall clock time: 21 minutes 40.50 seconds (1300.50 seconds total)