Starting phenix.real_space_refine
on Tue Mar  3 18:59:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7oz3_13119/03_2026/7oz3_13119.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oz3_13119/03_2026/7oz3_13119.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7oz3_13119/03_2026/7oz3_13119.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oz3_13119/03_2026/7oz3_13119.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oz3_13119/03_2026/7oz3_13119.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oz3_13119/03_2026/7oz3_13119.cif"
  }
  resolution = 4.46
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      92      5.49       5
     S       8      5.16       5
     C    4932      2.51       5
     N    1411      2.21       5
     O    1766      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  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: 8209
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1584
          Classifications: {'peptide': 202}
          Link IDs: {'PTRANS': 5, 'TRANS': 196}
    Chain: "B"
      Number of atoms: 1595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1595
          Classifications: {'peptide': 203}
          Link IDs: {'PTRANS': 5, 'TRANS': 197}
    Chain: "C"
      Number of atoms: 1580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1580
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 5, 'TRANS': 195}
    Chain: "D"
      Number of atoms: 1558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1558
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 5, 'TRANS': 192}
    Chain: "F"
      Number of atoms: 900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 900
          Classifications: {'DNA': 44}
          Link IDs: {'rna3p': 43}
    Chain: "G"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 904
          Classifications: {'DNA': 44}
          Link IDs: {'rna3p': 43}
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'2BA': 1}
          Classifications: {'RNA_mixed': 1}
    Chain: "B"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'2BA': 1}
          Classifications: {'RNA_mixed': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ARG C 210 " occ=0.75
      ... (9 atoms not shown)
      pdb=" NH2 ARG C 210 " occ=0.75
  Time building chain proxies: 1.93, per 1000 atoms: 0.24
  Number of scatterers: 8209
  At special positions: 0
  Unit cell: (77.404, 93.094, 161.084, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       8     16.00
     P      92     15.00
     O    1766      8.00
     N    1411      7.00
     C    4932      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: 0.82
  Conformation dependent library (CDL) restraints added in 310.9 milliseconds
  

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1504

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 9 sheets defined
      58.5% alpha, 9.7% beta
      44 base pairs and 82 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 27
    Processing helix  chain 'A' and resid 39 through 46
    Processing helix  chain 'A' and resid 48 through 62
      removed outlier: 3.528A  pdb=" N   LEU A  62 " --> pdb=" O   ILE A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 128
    Processing helix  chain 'A' and resid 129 through 132
    Processing helix  chain 'A' and resid 152 through 157
    Processing helix  chain 'A' and resid 157 through 163
    Processing helix  chain 'A' and resid 196 through 207
    Processing helix  chain 'B' and resid 11 through 27
    Processing helix  chain 'B' and resid 40 through 46
    Processing helix  chain 'B' and resid 48 through 62
      removed outlier: 4.067A  pdb=" N   LEU B  62 " --> pdb=" O   ILE B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 128
      removed outlier: 3.603A  pdb=" N   PHE B 122 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   LEU B 123 " --> pdb=" O   VAL B 119 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   LEU B 124 " --> pdb=" O   ASP B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 132
    Processing helix  chain 'B' and resid 152 through 157
    Processing helix  chain 'B' and resid 157 through 163
    Processing helix  chain 'B' and resid 196 through 207
    Processing helix  chain 'C' and resid 11 through 27
      removed outlier: 4.157A  pdb=" N   ILE C  16 " --> pdb=" O   LYS C  12 " (cutoff:3.500A)
      removed outlier: 5.115A  pdb=" N   ALA C  17 " --> pdb=" O   TYR C  13 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 37 through 46
    Processing helix  chain 'C' and resid 48 through 62
    Processing helix  chain 'C' and resid 77 through 92
      removed outlier: 4.144A  pdb=" N   ALA C  81 " --> pdb=" O   SER C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 94 through 127
      removed outlier: 3.712A  pdb=" N   ARG C 127 " --> pdb=" O   LEU C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 157
    Processing helix  chain 'C' and resid 157 through 163
    Processing helix  chain 'C' and resid 196 through 208
    Processing helix  chain 'D' and resid 14 through 26
    Processing helix  chain 'D' and resid 37 through 45
    Processing helix  chain 'D' and resid 48 through 62
    Processing helix  chain 'D' and resid 78 through 92
    Processing helix  chain 'D' and resid 94 through 126
    Processing helix  chain 'D' and resid 132 through 136
    Processing helix  chain 'D' and resid 153 through 157
    Processing helix  chain 'D' and resid 157 through 163
    Processing helix  chain 'D' and resid 196 through 207
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35
      removed outlier: 3.637A  pdb=" N   GLY A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 141
      removed outlier: 3.500A  pdb=" N   PHE A 193 " --> pdb=" O   TYR A 138 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   VAL A 194 " --> pdb=" O   ILE A 166 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   ILE A 166 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE A 169 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 35
    Processing sheet with id=AA4, first strand: chain 'B' and resid 140 through 141
      removed outlier: 6.586A  pdb=" N   VAL B 194 " --> pdb=" O   ILE B 166 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   ILE B 166 " --> pdb=" O   VAL B 194 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE B 169 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 65 through 66
      removed outlier: 3.610A  pdb=" N   ILE C  74 " --> pdb=" O   THR C  66 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 138 through 141
      removed outlier: 3.656A  pdb=" N   HIS C 190 " --> pdb=" O   GLU C 170 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   VAL C 194 " --> pdb=" O   ILE C 166 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   ILE C 166 " --> pdb=" O   VAL C 194 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 151 through 152
      removed outlier: 4.587A  pdb=" N   LYS C 151 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 138 through 141
      removed outlier: 6.462A  pdb=" N   VAL D 194 " --> pdb=" O   ILE D 166 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   ILE D 166 " --> pdb=" O   VAL D 194 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   HIS D 171 " --> pdb=" O   LYS D 174 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 151 through 152
      removed outlier: 4.588A  pdb=" N   LYS D 151 " --> pdb=" O   ILE D 185 " (cutoff:3.500A)

    383 hydrogen bonds defined for protein.
    1104 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      103 hydrogen bonds
      206 hydrogen bond angles
      0 basepair planarities
      44 basepair parallelities
      82 stacking parallelities
  Total time for adding SS restraints: 1.18

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1578
        1.33 -     1.45: 2406
        1.45 -     1.57: 4362
        1.57 -     1.69: 185
        1.69 -     1.81: 16
  Bond restraints: 8547
  Sorted by residual:
  bond pdb=" C1' 2BA A 301 "
       pdb=" C2' 2BA A 301 "
    ideal  model  delta    sigma   weight residual
    1.541  1.347  0.194 2.00e-02 2.50e+03 9.38e+01
  bond pdb=" C1' 2BA B 301 "
       pdb=" C2' 2BA B 301 "
    ideal  model  delta    sigma   weight residual
    1.541  1.347  0.194 2.00e-02 2.50e+03 9.38e+01
  bond pdb="C1'1 2BA A 301 "
       pdb="C2'1 2BA A 301 "
    ideal  model  delta    sigma   weight residual
    1.532  1.349  0.183 2.00e-02 2.50e+03 8.41e+01
  bond pdb="C1'1 2BA B 301 "
       pdb="C2'1 2BA B 301 "
    ideal  model  delta    sigma   weight residual
    1.532  1.349  0.183 2.00e-02 2.50e+03 8.38e+01
  bond pdb="C1'1 2BA B 301 "
       pdb="O4'1 2BA B 301 "
    ideal  model  delta    sigma   weight residual
    1.408  1.573 -0.165 2.00e-02 2.50e+03 6.84e+01
  ... (remaining 8542 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 10904
        2.27 -     4.54: 896
        4.54 -     6.82: 145
        6.82 -     9.09: 9
        9.09 -    11.36: 1
  Bond angle restraints: 11955
  Sorted by residual:
  angle pdb=" O3'  DA F  22 "
        pdb=" C3'  DA F  22 "
        pdb=" C2'  DA F  22 "
      ideal   model   delta    sigma   weight residual
     111.50  122.86  -11.36 1.50e+00 4.44e-01 5.74e+01
  angle pdb=" N   SER C 143 "
        pdb=" CA  SER C 143 "
        pdb=" C   SER C 143 "
      ideal   model   delta    sigma   weight residual
     111.69  103.91    7.78 1.23e+00 6.61e-01 4.00e+01
  angle pdb=" N   GLU D 147 "
        pdb=" CA  GLU D 147 "
        pdb=" C   GLU D 147 "
      ideal   model   delta    sigma   weight residual
     112.54  105.73    6.81 1.22e+00 6.72e-01 3.11e+01
  angle pdb=" N   GLU C 147 "
        pdb=" CA  GLU C 147 "
        pdb=" C   GLU C 147 "
      ideal   model   delta    sigma   weight residual
     112.54  105.75    6.79 1.22e+00 6.72e-01 3.09e+01
  angle pdb=" N   ILE B  41 "
        pdb=" CA  ILE B  41 "
        pdb=" C   ILE B  41 "
      ideal   model   delta    sigma   weight residual
     111.44  104.21    7.23 1.34e+00 5.57e-01 2.91e+01
  ... (remaining 11950 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.97: 3890
       19.97 -    39.94: 707
       39.94 -    59.91: 384
       59.91 -    79.88: 8
       79.88 -    99.85: 4
  Dihedral angle restraints: 4993
    sinusoidal: 2661
      harmonic: 2332
  Sorted by residual:
  dihedral pdb=" C   PHE A 207 "
           pdb=" N   PHE A 207 "
           pdb=" CA  PHE A 207 "
           pdb=" CB  PHE A 207 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.85   11.25     0      2.50e+00 1.60e-01 2.03e+01
  dihedral pdb=" C   PHE B 207 "
           pdb=" N   PHE B 207 "
           pdb=" CA  PHE B 207 "
           pdb=" CB  PHE B 207 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.83   11.23     0      2.50e+00 1.60e-01 2.02e+01
  dihedral pdb=" CA  ASN A 157 "
           pdb=" C   ASN A 157 "
           pdb=" N   VAL A 158 "
           pdb=" CA  VAL A 158 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.66  -18.34     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 4990 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1006
       0.082 -    0.165: 288
       0.165 -    0.247: 63
       0.247 -    0.329: 9
       0.329 -    0.411: 5
  Chirality restraints: 1371
  Sorted by residual:
  chirality pdb=" C2' 2BA A 301 "
            pdb=" C1' 2BA A 301 "
            pdb=" C3' 2BA A 301 "
            pdb=" O2' 2BA A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.80   -2.39   -0.41 2.00e-01 2.50e+01 4.23e+00
  chirality pdb=" C2' 2BA B 301 "
            pdb=" C1' 2BA B 301 "
            pdb=" C3' 2BA B 301 "
            pdb=" O2' 2BA B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.80   -2.40   -0.41 2.00e-01 2.50e+01 4.10e+00
  chirality pdb=" CA  PHE A 207 "
            pdb=" N   PHE A 207 "
            pdb=" C   PHE A 207 "
            pdb=" CB  PHE A 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.08e+00
  ... (remaining 1368 not shown)

  Planarity restraints: 1203
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  64 "   -0.016 2.00e-02 2.50e+03   3.21e-02 1.03e+01
        pdb=" C   ILE B  64 "    0.056 2.00e-02 2.50e+03
        pdb=" O   ILE B  64 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU B  65 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  70 "    0.015 2.00e-02 2.50e+03   2.98e-02 8.91e+00
        pdb=" C   GLY A  70 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   GLY A  70 "    0.019 2.00e-02 2.50e+03
        pdb=" N   SER A  71 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT F  19 "    0.001 2.00e-02 2.50e+03   1.84e-02 8.49e+00
        pdb=" N1   DT F  19 "    0.022 2.00e-02 2.50e+03
        pdb=" C2   DT F  19 "   -0.004 2.00e-02 2.50e+03
        pdb=" O2   DT F  19 "   -0.030 2.00e-02 2.50e+03
        pdb=" N3   DT F  19 "    0.006 2.00e-02 2.50e+03
        pdb=" C4   DT F  19 "    0.005 2.00e-02 2.50e+03
        pdb=" O4   DT F  19 "    0.015 2.00e-02 2.50e+03
        pdb=" C5   DT F  19 "    0.006 2.00e-02 2.50e+03
        pdb=" C7   DT F  19 "   -0.037 2.00e-02 2.50e+03
        pdb=" C6   DT F  19 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1200 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 2675
        2.85 -     3.36: 7752
        3.36 -     3.87: 14924
        3.87 -     4.39: 16813
        4.39 -     4.90: 25946
  Nonbonded interactions: 68110
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A  98 "
            pdb=" OD1 ASP B 120 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" OD1 ASP B  28 "
            pdb=" N   TYR B  29 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" O   ALA D 107 "
            pdb=" OE1 GLU D 111 "
     model   vdw
     2.381 3.040
  nonbonded pdb=" O   LEU A  85 "
            pdb=" OE1 GLU A  89 "
     model   vdw
     2.407 3.040
  nonbonded pdb=" O   LEU C 123 "
            pdb=" OG1 THR C 126 "
     model   vdw
     2.432 3.040
  ... (remaining 68105 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 13 through 209)
  selection = (chain 'B' and resid 13 through 209)
  selection = (chain 'C' and resid 13 through 209)
  selection = (chain 'D' and resid 13 through 209)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.75 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:             0.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     9.190
  Find NCS groups from input model:        0.120
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
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      :  0.011   0.194   8547  Z= 0.671
  Angle     :  1.273  11.360  11955  Z= 0.870
  Chirality :  0.079   0.411   1371
  Planarity :  0.005   0.038   1203
  Dihedral  : 23.029  99.849   3489
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  3.80 %
    Favored  : 95.91 %
  Cbeta Deviations :  0.27 %
  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:  0.64 (0.30), residues: 796
  helix:  1.86 (0.24), residues: 431
  sheet: -1.60 (0.54), residues: 72
  loop : -1.23 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 127 
 TYR   0.025   0.002   TYR A 206 
 PHE   0.019   0.002   PHE A 122 
 TRP   0.025   0.005   TRP B 159 
 HIS   0.004   0.001   HIS C 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.01086 ( 8547)
  covalent geometry    : angle       1.27289 (11955)
  hydrogen bonds       : bond        0.14259 (  486)
  hydrogen bonds       : angle       5.61186 ( 1310)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 182
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8328 (tp30) cc_final: 0.7812 (tp30)
REVERT: A  189 ASP cc_start: 0.8403 (m-30) cc_final: 0.7807 (m-30)
REVERT: A  207 PHE cc_start: 0.8466 (m-80) cc_final: 0.7295 (m-10)
REVERT: B  110 GLN cc_start: 0.8990 (mt0) cc_final: 0.8499 (mp10)
REVERT: B  121 ASP cc_start: 0.9039 (t70) cc_final: 0.8564 (t70)
REVERT: B  133 TYR cc_start: 0.8333 (p90) cc_final: 0.7765 (p90)
REVERT: B  189 ASP cc_start: 0.7421 (m-30) cc_final: 0.7169 (m-30)
REVERT: B  191 ILE cc_start: 0.9263 (mt) cc_final: 0.8887 (mt)
REVERT: C  190 HIS cc_start: 0.8223 (m-70) cc_final: 0.7519 (m170)
REVERT: D   26 ASN cc_start: 0.9393 (t0) cc_final: 0.8860 (t0)
REVERT: D   28 ASP cc_start: 0.8251 (m-30) cc_final: 0.7361 (m-30)
REVERT: D  142 VAL cc_start: 0.8832 (m) cc_final: 0.8517 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 184
  average time/residue: 0.0922
  time to fit residues: 22.7982
Evaluate side-chains
  87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.1980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 109 GLN
A 125 GLN
B 161 GLN
B 171 HIS
C  26 ASN
C  57 ASN
C  69 HIS
C  92 HIS
D  92 HIS
D 171 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.065053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.052338 restraints weight = 35857.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.053954 restraints weight = 19950.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.055071 restraints weight = 13185.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.055872 restraints weight = 9739.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.056360 restraints weight = 7757.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3017
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3017
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.2475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8547  Z= 0.171
  Angle     :  0.610   7.560  11955  Z= 0.361
  Chirality :  0.041   0.261   1371
  Planarity :  0.004   0.049   1203
  Dihedral  : 24.575  96.551   1969
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  5.41 %
    Favored  : 94.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.30), residues: 796
  helix:  2.12 (0.24), residues: 432
  sheet: -1.15 (0.55), residues: 68
  loop : -1.15 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  38 
 TYR   0.017   0.002   TYR D 200 
 PHE   0.019   0.002   PHE D 207 
 TRP   0.013   0.002   TRP C 159 
 HIS   0.016   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 8547)
  covalent geometry    : angle       0.61034 (11955)
  hydrogen bonds       : bond        0.04152 (  486)
  hydrogen bonds       : angle       4.37025 ( 1310)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  207 PHE cc_start: 0.8636 (m-80) cc_final: 0.7967 (m-10)
REVERT: B   22 GLN cc_start: 0.8893 (mt0) cc_final: 0.8568 (pt0)
REVERT: B   79 GLU cc_start: 0.8473 (mp0) cc_final: 0.7892 (pm20)
REVERT: B  109 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8030 (tm-30)
REVERT: B  110 GLN cc_start: 0.8965 (mt0) cc_final: 0.8480 (mp10)
REVERT: B  121 ASP cc_start: 0.9163 (t70) cc_final: 0.8492 (t0)
REVERT: B  133 TYR cc_start: 0.8182 (p90) cc_final: 0.7971 (p90)
REVERT: C   57 ASN cc_start: 0.8923 (m110) cc_final: 0.8638 (m110)
REVERT: C  112 MET cc_start: 0.8108 (tpp) cc_final: 0.7869 (tpp)
REVERT: C  190 HIS cc_start: 0.7805 (m-70) cc_final: 0.7398 (m170)
REVERT: C  192 PHE cc_start: 0.9015 (m-80) cc_final: 0.8702 (m-80)
REVERT: D   26 ASN cc_start: 0.9462 (t0) cc_final: 0.9138 (t0)
REVERT: D   28 ASP cc_start: 0.8355 (m-30) cc_final: 0.7932 (m-30)
REVERT: D   80 LYS cc_start: 0.9405 (mmtp) cc_final: 0.9081 (mttp)
REVERT: D  142 VAL cc_start: 0.8878 (m) cc_final: 0.8511 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0779
  time to fit residues: 13.6280
Evaluate side-chains
  76 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 45 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
B 171 HIS
C  26 ASN
D 108 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.063680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.051496 restraints weight = 35430.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.053059 restraints weight = 19804.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.054106 restraints weight = 13121.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.054953 restraints weight = 9722.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.055486 restraints weight = 7675.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3004
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3004
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8547  Z= 0.148
  Angle     :  0.574   6.860  11955  Z= 0.340
  Chirality :  0.039   0.165   1371
  Planarity :  0.004   0.050   1203
  Dihedral  : 24.647  86.860   1969
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  3.51 %
    Favored  : 96.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.30), residues: 796
  helix:  2.23 (0.24), residues: 434
  sheet: -0.87 (0.57), residues: 68
  loop : -0.95 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  38 
 TYR   0.022   0.002   TYR C 206 
 PHE   0.018   0.002   PHE A 122 
 TRP   0.013   0.002   TRP C 159 
 HIS   0.012   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8547)
  covalent geometry    : angle       0.57406 (11955)
  hydrogen bonds       : bond        0.03773 (  486)
  hydrogen bonds       : angle       4.19716 ( 1310)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 MET cc_start: 0.8997 (tpp) cc_final: 0.8561 (tpp)
REVERT: A  207 PHE cc_start: 0.8502 (m-80) cc_final: 0.7667 (m-10)
REVERT: B   79 GLU cc_start: 0.8424 (mp0) cc_final: 0.7898 (pm20)
REVERT: B  121 ASP cc_start: 0.9220 (t70) cc_final: 0.8347 (t70)
REVERT: B  133 TYR cc_start: 0.8308 (p90) cc_final: 0.7894 (p90)
REVERT: B  189 ASP cc_start: 0.7327 (m-30) cc_final: 0.7028 (m-30)
REVERT: C   57 ASN cc_start: 0.8860 (m110) cc_final: 0.8567 (m110)
REVERT: C   64 ILE cc_start: 0.8664 (mp) cc_final: 0.8409 (mp)
REVERT: C  190 HIS cc_start: 0.7681 (m-70) cc_final: 0.7409 (m170)
REVERT: D   26 ASN cc_start: 0.9404 (t0) cc_final: 0.9091 (t0)
REVERT: D   28 ASP cc_start: 0.8390 (m-30) cc_final: 0.7873 (m-30)
REVERT: D   80 LYS cc_start: 0.9383 (mmtp) cc_final: 0.9062 (mttp)
  outliers start: 2
  outliers final: 0
  residues processed: 115
  average time/residue: 0.0771
  time to fit residues: 12.6911
Evaluate side-chains
  79 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 56 optimal weight:    7.9990
   chunk 30 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 54 optimal weight:    8.9990
   chunk 39 optimal weight:    0.5980
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
B 110 GLN
B 171 HIS
C  26 ASN
D 108 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.062680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.050261 restraints weight = 36140.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.051850 restraints weight = 20125.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.052964 restraints weight = 13291.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.053705 restraints weight = 9777.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.054322 restraints weight = 7827.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2979
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2978 r_free = 0.2978    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2978
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.3430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8547  Z= 0.143
  Angle     :  0.548   6.991  11955  Z= 0.325
  Chirality :  0.039   0.199   1371
  Planarity :  0.003   0.036   1203
  Dihedral  : 24.276  74.936   1969
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.24 %
    Favored  : 95.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.30), residues: 796
  helix:  2.20 (0.24), residues: 435
  sheet: -0.69 (0.61), residues: 67
  loop : -0.96 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  23 
 TYR   0.015   0.001   TYR B  88 
 PHE   0.019   0.001   PHE A 122 
 TRP   0.014   0.002   TRP B 159 
 HIS   0.009   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8547)
  covalent geometry    : angle       0.54835 (11955)
  hydrogen bonds       : bond        0.03571 (  486)
  hydrogen bonds       : angle       4.09459 ( 1310)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 GLU cc_start: 0.8399 (mp0) cc_final: 0.7880 (pm20)
REVERT: B  133 TYR cc_start: 0.8127 (p90) cc_final: 0.7787 (p90)
REVERT: C   57 ASN cc_start: 0.8839 (m110) cc_final: 0.8489 (m110)
REVERT: D   26 ASN cc_start: 0.9328 (t0) cc_final: 0.9015 (t0)
REVERT: D   28 ASP cc_start: 0.8259 (m-30) cc_final: 0.7693 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0807
  time to fit residues: 12.3374
Evaluate side-chains
  81 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 67 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   chunk 53 optimal weight:    9.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 171 HIS
C  26 ASN
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.059161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.046796 restraints weight = 36698.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.048346 restraints weight = 20553.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.049421 restraints weight = 13650.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.050114 restraints weight = 10099.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.050686 restraints weight = 8183.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2877
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2877 r_free = 0.2877    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2877
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.3952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8547  Z= 0.192
  Angle     :  0.590   5.494  11955  Z= 0.346
  Chirality :  0.040   0.218   1371
  Planarity :  0.003   0.036   1203
  Dihedral  : 23.948  66.427   1969
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  4.24 %
    Favored  : 95.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.30), residues: 796
  helix:  2.17 (0.24), residues: 434
  sheet: -0.21 (0.65), residues: 67
  loop : -0.94 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 202 
 TYR   0.019   0.002   TYR B 200 
 PHE   0.021   0.002   PHE A 122 
 TRP   0.012   0.002   TRP A 159 
 HIS   0.009   0.001   HIS B 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 8547)
  covalent geometry    : angle       0.58993 (11955)
  hydrogen bonds       : bond        0.04128 (  486)
  hydrogen bonds       : angle       4.19449 ( 1310)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 HIS cc_start: 0.8743 (m90) cc_final: 0.7927 (m90)
REVERT: A  203 MET cc_start: 0.9129 (tpp) cc_final: 0.8264 (tpt)
REVERT: A  207 PHE cc_start: 0.8466 (m-10) cc_final: 0.8231 (m-10)
REVERT: B   79 GLU cc_start: 0.8506 (mp0) cc_final: 0.8121 (pm20)
REVERT: B  110 GLN cc_start: 0.9010 (mt0) cc_final: 0.8493 (mp10)
REVERT: B  133 TYR cc_start: 0.8117 (p90) cc_final: 0.7805 (p90)
REVERT: B  189 ASP cc_start: 0.7016 (m-30) cc_final: 0.6600 (m-30)
REVERT: C   57 ASN cc_start: 0.8889 (m110) cc_final: 0.8550 (m110)
REVERT: D   26 ASN cc_start: 0.9323 (t0) cc_final: 0.8976 (t0)
REVERT: D   28 ASP cc_start: 0.8396 (m-30) cc_final: 0.7740 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0949
  time to fit residues: 12.7432
Evaluate side-chains
  73 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0770
   chunk 59 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.7338

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 108 GLN
C  26 ASN
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 160 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.059925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.047658 restraints weight = 36473.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.049249 restraints weight = 20305.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.050318 restraints weight = 13426.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.051132 restraints weight = 9921.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.051606 restraints weight = 7885.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2913
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2913
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.4204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8547  Z= 0.142
  Angle     :  0.531   8.943  11955  Z= 0.312
  Chirality :  0.039   0.226   1371
  Planarity :  0.003   0.037   1203
  Dihedral  : 23.536  63.376   1969
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.30), residues: 796
  helix:  2.38 (0.24), residues: 434
  sheet: -0.05 (0.67), residues: 67
  loop : -0.94 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 202 
 TYR   0.011   0.001   TYR B  88 
 PHE   0.020   0.001   PHE A 122 
 TRP   0.011   0.002   TRP B 159 
 HIS   0.007   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8547)
  covalent geometry    : angle       0.53056 (11955)
  hydrogen bonds       : bond        0.03564 (  486)
  hydrogen bonds       : angle       4.00103 ( 1310)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 MET cc_start: 0.9084 (tpp) cc_final: 0.8100 (tpt)
REVERT: A  207 PHE cc_start: 0.8407 (m-10) cc_final: 0.8026 (m-10)
REVERT: B   38 ARG cc_start: 0.8968 (mtp180) cc_final: 0.8667 (mtm-85)
REVERT: B   79 GLU cc_start: 0.8411 (mp0) cc_final: 0.8027 (pm20)
REVERT: B  133 TYR cc_start: 0.8167 (p90) cc_final: 0.7880 (p90)
REVERT: C   57 ASN cc_start: 0.8848 (m110) cc_final: 0.8509 (m110)
REVERT: D   26 ASN cc_start: 0.9347 (t0) cc_final: 0.8928 (t0)
REVERT: D   28 ASP cc_start: 0.8379 (m-30) cc_final: 0.7658 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0861
  time to fit residues: 12.1705
Evaluate side-chains
  77 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 78 optimal weight:    0.0980
   chunk 71 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 17 optimal weight:    8.9990
   chunk 34 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 83 optimal weight:    5.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 108 GLN
B 148 HIS
C  26 ASN
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 160 HIS
D 161 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.058694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.046449 restraints weight = 37360.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.048042 restraints weight = 20627.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.049134 restraints weight = 13597.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.049902 restraints weight = 10033.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.050254 restraints weight = 8031.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.4465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8547  Z= 0.160
  Angle     :  0.556   8.202  11955  Z= 0.327
  Chirality :  0.040   0.230   1371
  Planarity :  0.003   0.037   1203
  Dihedral  : 23.263  59.695   1969
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.31), residues: 796
  helix:  2.35 (0.24), residues: 434
  sheet: -0.04 (0.67), residues: 67
  loop : -0.92 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 202 
 TYR   0.018   0.002   TYR C 206 
 PHE   0.021   0.002   PHE A 122 
 TRP   0.010   0.002   TRP C 159 
 HIS   0.007   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 8547)
  covalent geometry    : angle       0.55556 (11955)
  hydrogen bonds       : bond        0.03730 (  486)
  hydrogen bonds       : angle       4.11480 ( 1310)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 GLU cc_start: 0.8498 (mp0) cc_final: 0.8079 (pm20)
REVERT: B  124 LEU cc_start: 0.8733 (mm) cc_final: 0.8322 (tp)
REVERT: B  133 TYR cc_start: 0.8141 (p90) cc_final: 0.7871 (p90)
REVERT: B  189 ASP cc_start: 0.6994 (m-30) cc_final: 0.6342 (m-30)
REVERT: C   57 ASN cc_start: 0.8832 (m110) cc_final: 0.8488 (m110)
REVERT: D   26 ASN cc_start: 0.9308 (t0) cc_final: 0.8917 (t0)
REVERT: D   28 ASP cc_start: 0.8447 (m-30) cc_final: 0.7674 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0830
  time to fit residues: 11.5244
Evaluate side-chains
  73 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   chunk 26 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 67 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 81 optimal weight:    4.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 HIS
C  26 ASN
C 208 ASN
** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.059214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.047179 restraints weight = 36564.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.048687 restraints weight = 20525.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.049771 restraints weight = 13668.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.050505 restraints weight = 10156.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.051064 restraints weight = 8143.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2892
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2892
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.4684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8547  Z= 0.139
  Angle     :  0.531   6.914  11955  Z= 0.313
  Chirality :  0.039   0.210   1371
  Planarity :  0.003   0.039   1203
  Dihedral  : 23.112  59.920   1969
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  1.90 %
    Favored  : 97.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.30), residues: 796
  helix:  2.37 (0.24), residues: 434
  sheet:  0.05 (0.67), residues: 67
  loop : -0.93 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 202 
 TYR   0.011   0.001   TYR B  88 
 PHE   0.020   0.001   PHE A 122 
 TRP   0.040   0.004   TRP A 159 
 HIS   0.006   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8547)
  covalent geometry    : angle       0.53075 (11955)
  hydrogen bonds       : bond        0.03554 (  486)
  hydrogen bonds       : angle       4.02729 ( 1310)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 GLU cc_start: 0.8363 (mp0) cc_final: 0.8034 (pm20)
REVERT: B  124 LEU cc_start: 0.8700 (mm) cc_final: 0.8321 (tp)
REVERT: B  133 TYR cc_start: 0.8202 (p90) cc_final: 0.7901 (p90)
REVERT: C   57 ASN cc_start: 0.8787 (m110) cc_final: 0.8447 (m110)
REVERT: C  208 ASN cc_start: 0.6654 (OUTLIER) cc_final: 0.6443 (p0)
REVERT: D   26 ASN cc_start: 0.9331 (t0) cc_final: 0.8898 (t0)
REVERT: D   28 ASP cc_start: 0.8415 (m-30) cc_final: 0.7650 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 100
  average time/residue: 0.0911
  time to fit residues: 12.5775
Evaluate side-chains
  76 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 83 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A 108 GLN
C  26 ASN
D 108 GLN
D 171 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.058944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.046880 restraints weight = 37074.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.048339 restraints weight = 21674.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.049301 restraints weight = 14710.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.050020 restraints weight = 11176.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.050566 restraints weight = 9105.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2876
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2876
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.4788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8547  Z= 0.146
  Angle     :  0.544   9.055  11955  Z= 0.318
  Chirality :  0.039   0.192   1371
  Planarity :  0.003   0.038   1203
  Dihedral  : 22.971  59.272   1969
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.30), residues: 796
  helix:  2.35 (0.24), residues: 434
  sheet:  0.02 (0.67), residues: 67
  loop : -0.91 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 202 
 TYR   0.019   0.001   TYR C 206 
 PHE   0.021   0.001   PHE A 122 
 TRP   0.038   0.004   TRP A 159 
 HIS   0.007   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8547)
  covalent geometry    : angle       0.54406 (11955)
  hydrogen bonds       : bond        0.03646 (  486)
  hydrogen bonds       : angle       4.08701 ( 1310)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 MET cc_start: 0.8813 (tpt) cc_final: 0.8584 (tpt)
REVERT: B   79 GLU cc_start: 0.8412 (mp0) cc_final: 0.8067 (pm20)
REVERT: B  124 LEU cc_start: 0.8740 (mm) cc_final: 0.8334 (tp)
REVERT: B  133 TYR cc_start: 0.8154 (p90) cc_final: 0.7874 (p90)
REVERT: C   57 ASN cc_start: 0.8804 (m110) cc_final: 0.8464 (m110)
REVERT: D   26 ASN cc_start: 0.9328 (t0) cc_final: 0.8887 (t0)
REVERT: D   28 ASP cc_start: 0.8459 (m-30) cc_final: 0.7650 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0983
  time to fit residues: 12.8473
Evaluate side-chains
  75 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
C  26 ASN
** D 187 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 = 0.3082 r_free = 0.3082 target = 0.057598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.045339 restraints weight = 37440.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.046908 restraints weight = 20814.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.048019 restraints weight = 13758.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.048766 restraints weight = 10172.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.049329 restraints weight = 8172.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2851
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2851
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.5096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8547  Z= 0.162
  Angle     :  0.562   8.477  11955  Z= 0.326
  Chirality :  0.040   0.148   1371
  Planarity :  0.003   0.037   1203
  Dihedral  : 22.749  59.888   1969
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.30), residues: 796
  helix:  2.25 (0.24), residues: 440
  sheet: -0.04 (0.68), residues: 66
  loop : -0.96 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 202 
 TYR   0.013   0.001   TYR A  13 
 PHE   0.024   0.002   PHE C 175 
 TRP   0.034   0.003   TRP A 159 
 HIS   0.006   0.001   HIS A 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 8547)
  covalent geometry    : angle       0.56169 (11955)
  hydrogen bonds       : bond        0.03920 (  486)
  hydrogen bonds       : angle       4.19101 ( 1310)

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

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

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1592 Ramachandran restraints generated.
    796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 GLU cc_start: 0.8549 (mp0) cc_final: 0.8051 (pm20)
REVERT: B  124 LEU cc_start: 0.8572 (mm) cc_final: 0.8145 (tp)
REVERT: B  133 TYR cc_start: 0.8190 (p90) cc_final: 0.7897 (p90)
REVERT: C   57 ASN cc_start: 0.8837 (m110) cc_final: 0.8486 (m110)
REVERT: C  112 MET cc_start: 0.8228 (tpp) cc_final: 0.7982 (tpp)
REVERT: D   26 ASN cc_start: 0.9299 (t0) cc_final: 0.8834 (t0)
REVERT: D   28 ASP cc_start: 0.8542 (m-30) cc_final: 0.7726 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0871
  time to fit residues: 11.8367
Evaluate side-chains
  76 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 66 optimal weight:    0.2980
   chunk 62 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 46 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  26 ASN
C 190 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.058669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.046408 restraints weight = 36871.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.047996 restraints weight = 20461.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.049116 restraints weight = 13496.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.049874 restraints weight = 9947.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.050455 restraints weight = 7957.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2881
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2881 r_free = 0.2881    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2881
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.5162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8547  Z= 0.134
  Angle     :  0.552   8.665  11955  Z= 0.321
  Chirality :  0.039   0.182   1371
  Planarity :  0.003   0.038   1203
  Dihedral  : 22.743  59.972   1969
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.30), residues: 796
  helix:  2.26 (0.24), residues: 446
  sheet: -0.09 (0.67), residues: 66
  loop : -1.02 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 202 
 TYR   0.011   0.001   TYR B  88 
 PHE   0.019   0.001   PHE A 122 
 TRP   0.033   0.004   TRP A 159 
 HIS   0.005   0.001   HIS A 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8547)
  covalent geometry    : angle       0.55206 (11955)
  hydrogen bonds       : bond        0.03736 (  486)
  hydrogen bonds       : angle       4.11775 ( 1310)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1218.49 seconds
wall clock time: 21 minutes 47.16 seconds (1307.16 seconds total)