Starting phenix.real_space_refine
on Sat Apr  4 21:53:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ig8_52849/04_2026/9ig8_52849.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ig8_52849/04_2026/9ig8_52849.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ig8_52849/04_2026/9ig8_52849.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ig8_52849/04_2026/9ig8_52849.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ig8_52849/04_2026/9ig8_52849.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ig8_52849/04_2026/9ig8_52849.cif"
  }
  resolution = 4.41
  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=   0.001 sd=   0.010
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: 4
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    2663      2.51       5
     N     736      2.21       5
     O     830      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4251
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2127
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2127
          Classifications: {'peptide': 267}
          Link IDs: {'PTRANS': 12, 'TRANS': 254}
    Chain: "B"
      Number of atoms: 2124
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2124
          Classifications: {'peptide': 267}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 254}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.14, per 1000 atoms: 0.27
  Number of scatterers: 4251
  At special positions: 0
  Unit cell: (79.104, 91.464, 80.752, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      22     16.00
     O     830      8.00
     N     736      7.00
     C    2663      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: 0.33
  Conformation dependent library (CDL) restraints added in 169.5 milliseconds
  

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1028

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 6 sheets defined
      38.4% alpha, 27.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 75 through 81
    Processing helix  chain 'A' and resid 82 through 87
    Processing helix  chain 'A' and resid 97 through 101
    Processing helix  chain 'A' and resid 102 through 104
      No H-bonds generated for 'chain 'A' and resid 102 through 104'
    Processing helix  chain 'A' and resid 119 through 133
      removed outlier: 3.777A  pdb=" N   ASP A 133 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 173
    Processing helix  chain 'A' and resid 178 through 183
      removed outlier: 3.569A  pdb=" N   GLN A 183 " --> pdb=" O   VAL A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 202
    Processing helix  chain 'A' and resid 213 through 229
      removed outlier: 3.726A  pdb=" N   GLU A 217 " --> pdb=" O   ASP A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 267
    Processing helix  chain 'B' and resid 75 through 81
    Processing helix  chain 'B' and resid 82 through 86
    Processing helix  chain 'B' and resid 99 through 101
      No H-bonds generated for 'chain 'B' and resid 99 through 101'
    Processing helix  chain 'B' and resid 102 through 104
      No H-bonds generated for 'chain 'B' and resid 102 through 104'
    Processing helix  chain 'B' and resid 119 through 132
    Processing helix  chain 'B' and resid 169 through 173
    Processing helix  chain 'B' and resid 178 through 183
    Processing helix  chain 'B' and resid 188 through 202
    Processing helix  chain 'B' and resid 207 through 211
      removed outlier: 3.712A  pdb=" N   ARG B 210 " --> pdb=" O   ASN B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 228
    Processing helix  chain 'B' and resid 234 through 238
      removed outlier: 3.663A  pdb=" N   ASP B 237 " --> pdb=" O   THR B 234 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLN B 238 " --> pdb=" O   ALA B 235 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 234 through 238'
    Processing helix  chain 'B' and resid 247 through 267
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 11
      removed outlier: 8.310A  pdb=" N   ALA A   3 " --> pdb=" O   SER A  22 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   SER A  22 " --> pdb=" O   ALA A   3 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   TRP A   5 " --> pdb=" O   VAL A  20 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   THR A 166 " --> pdb=" O   ASP A 107 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   SER A 109 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   VAL A 164 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
      removed outlier: 5.616A  pdb=" N   PHE A 111 " --> pdb=" O   MET A 162 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   MET A 162 " --> pdb=" O   PHE A 111 " (cutoff:3.500A)
      removed outlier: 8.885A  pdb=" N   GLU A 113 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
      removed outlier: 12.559A  pdb=" N   GLU A 160 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   LEU A 148 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA A 136 " --> pdb=" O   LEU A 151 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   HIS A 139 " --> pdb=" O   VAL A  92 " (cutoff:3.500A)
      removed outlier: 5.764A  pdb=" N   VAL A  92 " --> pdb=" O   HIS A 139 " (cutoff:3.500A)
      removed outlier: 8.817A  pdb=" N   THR A 141 " --> pdb=" O   ILE A  90 " (cutoff:3.500A)
      removed outlier: 8.132A  pdb=" N   ILE A  90 " --> pdb=" O   THR A 141 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41
      removed outlier: 4.068A  pdb=" N   VAL A  34 " --> pdb=" O   ALA B  61 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ALA B  61 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44
    Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 48
      removed outlier: 3.534A  pdb=" N   VAL A  47 " --> pdb=" O   ARG B  43 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG B  43 " --> pdb=" O   VAL A  47 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 60 through 63
    Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 11
      removed outlier: 7.773A  pdb=" N   ALA B   3 " --> pdb=" O   SER B  22 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   SER B  22 " --> pdb=" O   ALA B   3 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   TRP B   5 " --> pdb=" O   VAL B  20 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ARG B 108 " --> pdb=" O   THR B 166 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   MET B 162 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)
      removed outlier: 12.492A  pdb=" N   GLU B 160 " --> pdb=" O   PRO B 114 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   LEU B 148 " --> pdb=" O   LEU B 167 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   VAL B 153 " --> pdb=" O   ARG B 134 " (cutoff:3.500A)
      removed outlier: 10.008A  pdb=" N   ARG B 134 " --> pdb=" O   VAL B 153 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   GLU B  94 " --> pdb=" O   ILE B 137 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   HIS B 139 " --> pdb=" O   VAL B  92 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   VAL B  92 " --> pdb=" O   HIS B 139 " (cutoff:3.500A)
      removed outlier: 9.223A  pdb=" N   THR B 141 " --> pdb=" O   ILE B  90 " (cutoff:3.500A)
      removed outlier: 8.203A  pdb=" N   ILE B  90 " --> pdb=" O   THR B 141 " (cutoff:3.500A)

    205 hydrogen bonds defined for protein.
    543 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.61

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1455
        1.34 -     1.46: 788
        1.46 -     1.58: 2046
        1.58 -     1.70: 0
        1.70 -     1.82: 40
  Bond restraints: 4329
  Sorted by residual:
  bond pdb=" C   GLN A 238 "
       pdb=" N   PRO A 239 "
    ideal  model  delta    sigma   weight residual
    1.326  1.361 -0.034 1.44e-02 4.82e+03 5.69e+00
  bond pdb=" N   VAL B 123 "
       pdb=" CA  VAL B 123 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.025 1.25e-02 6.40e+03 3.87e+00
  bond pdb=" N   LEU B 124 "
       pdb=" CA  LEU B 124 "
    ideal  model  delta    sigma   weight residual
    1.457  1.477 -0.019 1.29e-02 6.01e+03 2.24e+00
  bond pdb=" CA  LEU A 181 "
       pdb=" C   LEU A 181 "
    ideal  model  delta    sigma   weight residual
    1.522  1.541 -0.019 1.38e-02 5.25e+03 1.81e+00
  bond pdb=" N   LEU B 125 "
       pdb=" CA  LEU B 125 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.29e-02 6.01e+03 1.75e+00
  ... (remaining 4324 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 5593
        1.73 -     3.46: 208
        3.46 -     5.19: 29
        5.19 -     6.92: 20
        6.92 -     8.65: 4
  Bond angle restraints: 5854
  Sorted by residual:
  angle pdb=" N   LYS B 158 "
        pdb=" CA  LYS B 158 "
        pdb=" C   LYS B 158 "
      ideal   model   delta    sigma   weight residual
     114.56  109.90    4.66 1.27e+00 6.20e-01 1.34e+01
  angle pdb=" N   GLU A  49 "
        pdb=" CA  GLU A  49 "
        pdb=" C   GLU A  49 "
      ideal   model   delta    sigma   weight residual
     114.04  109.90    4.14 1.24e+00 6.50e-01 1.12e+01
  angle pdb=" CA  GLU A 160 "
        pdb=" CB  GLU A 160 "
        pdb=" CG  GLU A 160 "
      ideal   model   delta    sigma   weight residual
     114.10  120.68   -6.58 2.00e+00 2.50e-01 1.08e+01
  angle pdb=" CA  GLN B  33 "
        pdb=" CB  GLN B  33 "
        pdb=" CG  GLN B  33 "
      ideal   model   delta    sigma   weight residual
     114.10  120.26   -6.16 2.00e+00 2.50e-01 9.48e+00
  angle pdb=" CB  GLU A 160 "
        pdb=" CG  GLU A 160 "
        pdb=" CD  GLU A 160 "
      ideal   model   delta    sigma   weight residual
     112.60  117.63   -5.03 1.70e+00 3.46e-01 8.75e+00
  ... (remaining 5849 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 2330
       17.81 -    35.61: 270
       35.61 -    53.42: 53
       53.42 -    71.22: 14
       71.22 -    89.02: 9
  Dihedral angle restraints: 2676
    sinusoidal: 1100
      harmonic: 1576
  Sorted by residual:
  dihedral pdb=" CA  ARG B 147 "
           pdb=" C   ARG B 147 "
           pdb=" N   LEU B 148 "
           pdb=" CA  LEU B 148 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.91   25.09     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  HIS A  35 "
           pdb=" C   HIS A  35 "
           pdb=" N   ALA A  36 "
           pdb=" CA  ALA A  36 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.94  -17.06     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CB  GLU B 236 "
           pdb=" CG  GLU B 236 "
           pdb=" CD  GLU B 236 "
           pdb=" OE1 GLU B 236 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.02   89.02     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 2673 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 472
       0.050 -    0.100: 140
       0.100 -    0.151: 31
       0.151 -    0.201: 2
       0.201 -    0.251: 4
  Chirality restraints: 649
  Sorted by residual:
  chirality pdb=" CA  LEU B 124 "
            pdb=" N   LEU B 124 "
            pdb=" C   LEU B 124 "
            pdb=" CB  LEU B 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CA  LEU B 125 "
            pdb=" N   LEU B 125 "
            pdb=" C   LEU B 125 "
            pdb=" CB  LEU B 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CB  ILE B  90 "
            pdb=" CA  ILE B  90 "
            pdb=" CG1 ILE B  90 "
            pdb=" CG2 ILE B  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 646 not shown)

  Planarity restraints: 774
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 122 "    0.011 2.00e-02 2.50e+03   2.33e-02 5.41e+00
        pdb=" C   TYR B 122 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   TYR B 122 "    0.015 2.00e-02 2.50e+03
        pdb=" N   VAL B 123 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B 200 "   -0.009 2.00e-02 2.50e+03   1.85e-02 3.41e+00
        pdb=" CG  ASP B 200 "    0.032 2.00e-02 2.50e+03
        pdb=" OD1 ASP B 200 "   -0.011 2.00e-02 2.50e+03
        pdb=" OD2 ASP B 200 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 200 "    0.008 2.00e-02 2.50e+03   1.67e-02 2.79e+00
        pdb=" CG  ASP A 200 "   -0.029 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 200 "    0.010 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 200 "    0.010 2.00e-02 2.50e+03
  ... (remaining 771 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 1704
        2.89 -     3.39: 4548
        3.39 -     3.90: 7343
        3.90 -     4.40: 8374
        4.40 -     4.90: 12880
  Nonbonded interactions: 34849
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 125 "
            pdb=" OG1 THR B 128 "
     model   vdw
     2.390 3.040
  nonbonded pdb=" O   VAL B 123 "
            pdb=" C   LEU B 124 "
     model   vdw
     2.405 3.270
  nonbonded pdb=" O   LEU B 125 "
            pdb=" C   ALA B 126 "
     model   vdw
     2.466 3.270
  nonbonded pdb=" N   GLN B  33 "
            pdb=" OE1 GLN B  33 "
     model   vdw
     2.523 3.120
  nonbonded pdb=" O   LEU B 125 "
            pdb=" N   THR B 128 "
     model   vdw
     2.525 3.120
  ... (remaining 34844 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 1 through 123 or (resid 124 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 125 through 267))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  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:                     6.110
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.000
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
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      :  0.003   0.038   4329  Z= 0.178
  Angle     :  0.836   8.651   5854  Z= 0.460
  Chirality :  0.051   0.251    649
  Planarity :  0.004   0.039    774
  Dihedral  : 16.451  89.024   1648
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 16.14
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.40 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 26.46 %
    Favored  : 71.37 %
  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: -0.52 (0.38), residues: 530
  helix:  0.39 (0.41), residues: 170
  sheet: -0.68 (0.52), residues: 92
  loop : -0.61 (0.42), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  86 
 TYR   0.012   0.001   TYR A 122 
 PHE   0.007   0.001   PHE A 111 
 TRP   0.008   0.001   TRP A 169 
 HIS   0.003   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4329)
  covalent geometry    : angle       0.83576 ( 5854)
  hydrogen bonds       : bond        0.15760 (  205)
  hydrogen bonds       : angle       8.30553 (  543)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 MET cc_start: 0.8039 (ptp) cc_final: 0.6052 (ptp)
REVERT: A  194 MET cc_start: 0.9421 (ptp) cc_final: 0.9121 (ptm)
REVERT: A  222 LEU cc_start: 0.9819 (tt) cc_final: 0.9605 (pp)
REVERT: B  222 LEU cc_start: 0.9776 (tp) cc_final: 0.9518 (tt)
REVERT: B  233 PHE cc_start: 0.8250 (m-80) cc_final: 0.7104 (m-80)
  outliers start: 10
  outliers final: 8
  residues processed: 49
  average time/residue: 0.0550
  time to fit residues: 3.5834
Evaluate side-chains
  45 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    9.9990
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 50 optimal weight:    0.0570
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   overall best weight:    2.1302

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

Flipped N/Q/H residues before XYZ refinement:
B 139 HIS
B 197 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.047444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.034470 restraints weight = 30739.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.035815 restraints weight = 18598.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.036715 restraints weight = 13593.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.037305 restraints weight = 11070.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.037760 restraints weight = 9677.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4329  Z= 0.173
  Angle     :  0.609   5.319   5854  Z= 0.329
  Chirality :  0.047   0.185    649
  Planarity :  0.004   0.039    774
  Dihedral  :  4.721  18.696    586
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 16.49
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.58 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.38 (0.38), residues: 530
  helix:  0.47 (0.40), residues: 170
  sheet: -0.69 (0.46), residues: 118
  loop : -0.39 (0.45), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 262 
 TYR   0.015   0.002   TYR A 122 
 PHE   0.018   0.002   PHE A  95 
 TRP   0.004   0.001   TRP B   5 
 HIS   0.003   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 4329)
  covalent geometry    : angle       0.60901 ( 5854)
  hydrogen bonds       : bond        0.04053 (  205)
  hydrogen bonds       : angle       6.59047 (  543)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 MET cc_start: 0.9357 (ppp) cc_final: 0.9090 (ppp)
REVERT: A  163 MET cc_start: 0.8027 (ptp) cc_final: 0.7217 (ptp)
REVERT: A  194 MET cc_start: 0.9348 (ptp) cc_final: 0.9043 (ptm)
REVERT: B  105 MET cc_start: 0.9338 (mmm) cc_final: 0.8716 (mpp)
REVERT: B  162 MET cc_start: 0.9122 (ptp) cc_final: 0.8838 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0588
  time to fit residues: 4.1232
Evaluate side-chains
  32 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 49 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9990
   chunk 32 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 165 HIS
B 139 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.047699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.034269 restraints weight = 31193.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.035664 restraints weight = 19017.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.036600 restraints weight = 13905.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.037168 restraints weight = 11331.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.037620 restraints weight = 9959.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4329  Z= 0.150
  Angle     :  0.568   5.562   5854  Z= 0.305
  Chirality :  0.046   0.197    649
  Planarity :  0.004   0.038    774
  Dihedral  :  4.473  16.769    586
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.15 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  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: -0.28 (0.37), residues: 530
  helix:  0.64 (0.40), residues: 170
  sheet: -0.63 (0.46), residues: 118
  loop : -0.41 (0.43), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  30 
 TYR   0.016   0.002   TYR A 122 
 PHE   0.007   0.001   PHE B  31 
 TRP   0.003   0.001   TRP B   5 
 HIS   0.003   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 4329)
  covalent geometry    : angle       0.56783 ( 5854)
  hydrogen bonds       : bond        0.03656 (  205)
  hydrogen bonds       : angle       6.04234 (  543)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 MET cc_start: 0.9427 (ppp) cc_final: 0.9034 (ppp)
REVERT: A  163 MET cc_start: 0.9123 (ptm) cc_final: 0.6454 (ptp)
REVERT: A  194 MET cc_start: 0.9328 (ptp) cc_final: 0.9108 (ptm)
REVERT: B   21 TYR cc_start: 0.9007 (m-10) cc_final: 0.8354 (m-10)
REVERT: B  233 PHE cc_start: 0.8551 (m-80) cc_final: 0.8094 (m-80)
REVERT: B  263 SER cc_start: 0.9287 (t) cc_final: 0.9002 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0527
  time to fit residues: 3.2674
Evaluate side-chains
  32 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 51 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 26 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 9 optimal weight:    0.4980
   chunk 42 optimal weight:    1.9990
   overall best weight:    2.6986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.046218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.033209 restraints weight = 30404.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.034529 restraints weight = 18620.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.035434 restraints weight = 13670.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.036045 restraints weight = 11163.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.036471 restraints weight = 9771.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4329  Z= 0.206
  Angle     :  0.606   7.666   5854  Z= 0.325
  Chirality :  0.046   0.164    649
  Planarity :  0.005   0.041    774
  Dihedral  :  4.807  16.498    586
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 17.20
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.72 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.41 (0.38), residues: 530
  helix:  0.67 (0.40), residues: 170
  sheet: -0.86 (0.44), residues: 130
  loop : -0.48 (0.44), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 262 
 TYR   0.016   0.002   TYR A 122 
 PHE   0.009   0.002   PHE B  31 
 TRP   0.006   0.001   TRP B   5 
 HIS   0.003   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 4329)
  covalent geometry    : angle       0.60582 ( 5854)
  hydrogen bonds       : bond        0.03763 (  205)
  hydrogen bonds       : angle       6.05501 (  543)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   94 GLU cc_start: 0.8874 (pt0) cc_final: 0.8442 (pt0)
REVERT: B  105 MET cc_start: 0.9365 (mpp) cc_final: 0.8888 (mpp)
REVERT: B  194 MET cc_start: 0.9312 (ptp) cc_final: 0.9057 (ptm)
REVERT: B  233 PHE cc_start: 0.8676 (m-80) cc_final: 0.8251 (m-80)
REVERT: B  263 SER cc_start: 0.9323 (t) cc_final: 0.9046 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.0568
  time to fit residues: 3.4203
Evaluate side-chains
  33 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 50 optimal weight:   20.0000
   chunk 45 optimal weight:    8.9990
   chunk 29 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0170
   overall best weight:    1.5422

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.047327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.034445 restraints weight = 31319.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.035812 restraints weight = 19144.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.036736 restraints weight = 14053.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.037347 restraints weight = 11481.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.037772 restraints weight = 10058.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.3738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4329  Z= 0.137
  Angle     :  0.555   5.998   5854  Z= 0.295
  Chirality :  0.046   0.156    649
  Planarity :  0.004   0.040    774
  Dihedral  :  4.499  16.106    586
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  3.96 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  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: -0.34 (0.37), residues: 530
  helix:  0.64 (0.40), residues: 170
  sheet: -0.76 (0.46), residues: 118
  loop : -0.44 (0.43), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 262 
 TYR   0.013   0.001   TYR A 122 
 PHE   0.007   0.001   PHE A 140 
 TRP   0.005   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4329)
  covalent geometry    : angle       0.55464 ( 5854)
  hydrogen bonds       : bond        0.03427 (  205)
  hydrogen bonds       : angle       5.89845 (  543)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.9547 (ptm) cc_final: 0.9169 (ptm)
REVERT: B  105 MET cc_start: 0.9474 (mpp) cc_final: 0.9054 (mpp)
REVERT: B  194 MET cc_start: 0.9390 (ptp) cc_final: 0.9100 (ptm)
REVERT: B  233 PHE cc_start: 0.8703 (m-80) cc_final: 0.8276 (m-80)
REVERT: B  263 SER cc_start: 0.9313 (t) cc_final: 0.9051 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0609
  time to fit residues: 3.4502
Evaluate side-chains
  31 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 34 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 25 optimal weight:   10.0000
   chunk 12 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   overall best weight:    2.0986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.046412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.033663 restraints weight = 31884.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.035002 restraints weight = 19322.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.035949 restraints weight = 13981.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.036582 restraints weight = 11257.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.037004 restraints weight = 9739.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.4066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4329  Z= 0.165
  Angle     :  0.569   5.293   5854  Z= 0.304
  Chirality :  0.047   0.265    649
  Planarity :  0.004   0.049    774
  Dihedral  :  4.649  18.782    586
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.15 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.37), residues: 530
  helix:  0.74 (0.40), residues: 170
  sheet: -0.74 (0.46), residues: 118
  loop : -0.50 (0.42), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 262 
 TYR   0.012   0.002   TYR A 122 
 PHE   0.008   0.001   PHE A 140 
 TRP   0.004   0.001   TRP B   5 
 HIS   0.002   0.001   HIS B 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4329)
  covalent geometry    : angle       0.56890 ( 5854)
  hydrogen bonds       : bond        0.03515 (  205)
  hydrogen bonds       : angle       5.80842 (  543)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 MET cc_start: 0.9389 (ppp) cc_final: 0.8889 (ppp)
REVERT: A  194 MET cc_start: 0.9525 (ptm) cc_final: 0.9163 (ptm)
REVERT: B   94 GLU cc_start: 0.8888 (pt0) cc_final: 0.8544 (pt0)
REVERT: B  105 MET cc_start: 0.9370 (mpp) cc_final: 0.9053 (mpp)
REVERT: B  194 MET cc_start: 0.9354 (ptp) cc_final: 0.9095 (ptm)
REVERT: B  233 PHE cc_start: 0.8752 (m-80) cc_final: 0.8286 (m-80)
REVERT: B  263 SER cc_start: 0.9343 (t) cc_final: 0.9085 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0799
  time to fit residues: 4.3215
Evaluate side-chains
  33 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   chunk 13 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 1 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 26 optimal weight:    8.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
B 139 HIS
B 197 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.047326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.034339 restraints weight = 31735.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.035741 restraints weight = 19302.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.036713 restraints weight = 14006.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.037360 restraints weight = 11315.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.037793 restraints weight = 9819.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.4275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4329  Z= 0.126
  Angle     :  0.555   6.705   5854  Z= 0.295
  Chirality :  0.046   0.191    649
  Planarity :  0.004   0.044    774
  Dihedral  :  4.509  17.014    586
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.26 (0.37), residues: 530
  helix:  0.69 (0.40), residues: 170
  sheet: -0.73 (0.46), residues: 118
  loop : -0.37 (0.43), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  62 
 TYR   0.012   0.001   TYR A 122 
 PHE   0.007   0.001   PHE A 140 
 TRP   0.001   0.000   TRP A   5 
 HIS   0.002   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 4329)
  covalent geometry    : angle       0.55487 ( 5854)
  hydrogen bonds       : bond        0.03348 (  205)
  hydrogen bonds       : angle       5.80409 (  543)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.9516 (ptm) cc_final: 0.9161 (ptm)
REVERT: B   94 GLU cc_start: 0.8904 (pt0) cc_final: 0.8391 (pt0)
REVERT: B  105 MET cc_start: 0.9408 (mpp) cc_final: 0.9129 (mpp)
REVERT: B  163 MET cc_start: 0.8605 (ptm) cc_final: 0.8404 (ptp)
REVERT: B  194 MET cc_start: 0.9352 (ptp) cc_final: 0.9146 (ptm)
REVERT: B  233 PHE cc_start: 0.8773 (m-80) cc_final: 0.8330 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0522
  time to fit residues: 2.8692
Evaluate side-chains
  30 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 51 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 20 optimal weight:    9.9990
   chunk 22 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   chunk 11 optimal weight:    0.3980
   chunk 25 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    1.0582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.047093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.034102 restraints weight = 31666.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.035486 restraints weight = 19129.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.036479 restraints weight = 13781.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.037120 restraints weight = 11075.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.037540 restraints weight = 9604.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.4473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   4329  Z= 0.116
  Angle     :  0.557   7.963   5854  Z= 0.291
  Chirality :  0.047   0.335    649
  Planarity :  0.004   0.040    774
  Dihedral  :  4.453  20.705    586
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  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: -0.20 (0.38), residues: 530
  helix:  0.90 (0.40), residues: 170
  sheet: -1.07 (0.48), residues: 110
  loop : -0.28 (0.42), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 262 
 TYR   0.011   0.001   TYR A 122 
 PHE   0.008   0.001   PHE B  95 
 TRP   0.001   0.000   TRP A 169 
 HIS   0.002   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 4329)
  covalent geometry    : angle       0.55728 ( 5854)
  hydrogen bonds       : bond        0.03187 (  205)
  hydrogen bonds       : angle       5.57562 (  543)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.9258 (mmm) cc_final: 0.8751 (mpp)
REVERT: A  162 MET cc_start: 0.9156 (ptp) cc_final: 0.8871 (ptp)
REVERT: A  194 MET cc_start: 0.9526 (ptm) cc_final: 0.9198 (ptm)
REVERT: B   33 GLN cc_start: 0.9320 (pm20) cc_final: 0.9097 (mm-40)
REVERT: B   64 TYR cc_start: 0.8482 (t80) cc_final: 0.8207 (t80)
REVERT: B  194 MET cc_start: 0.9366 (ptp) cc_final: 0.9164 (ptm)
REVERT: B  233 PHE cc_start: 0.8788 (m-80) cc_final: 0.8352 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0554
  time to fit residues: 3.3053
Evaluate side-chains
  32 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 10 optimal weight:    0.4980
   chunk 27 optimal weight:    8.9990
   chunk 46 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0370
   chunk 50 optimal weight:   30.0000
   chunk 30 optimal weight:   10.0000
   chunk 7 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.2060

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

Flipped N/Q/H residues before XYZ refinement:
B 197 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.046856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.034018 restraints weight = 31114.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.035398 restraints weight = 18838.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.036385 restraints weight = 13480.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.037026 restraints weight = 10776.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.037304 restraints weight = 9280.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.4713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4329  Z= 0.119
  Angle     :  0.554   8.087   5854  Z= 0.287
  Chirality :  0.046   0.298    649
  Planarity :  0.004   0.041    774
  Dihedral  :  4.368  16.781    586
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  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: -0.13 (0.38), residues: 530
  helix:  1.03 (0.40), residues: 168
  sheet: -1.03 (0.48), residues: 110
  loop : -0.28 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 262 
 TYR   0.012   0.001   TYR B 122 
 PHE   0.016   0.001   PHE A  11 
 TRP   0.002   0.000   TRP A 169 
 HIS   0.003   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 4329)
  covalent geometry    : angle       0.55435 ( 5854)
  hydrogen bonds       : bond        0.03136 (  205)
  hydrogen bonds       : angle       5.56019 (  543)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.9543 (ptm) cc_final: 0.9203 (ptm)
REVERT: B   33 GLN cc_start: 0.9310 (pm20) cc_final: 0.9086 (mm-40)
REVERT: B   64 TYR cc_start: 0.8503 (t80) cc_final: 0.8230 (t80)
REVERT: B   94 GLU cc_start: 0.9153 (pm20) cc_final: 0.8674 (pt0)
REVERT: B  111 PHE cc_start: 0.9028 (m-10) cc_final: 0.8640 (m-10)
REVERT: B  162 MET cc_start: 0.9254 (ptp) cc_final: 0.9034 (ptp)
REVERT: B  233 PHE cc_start: 0.8788 (m-80) cc_final: 0.8372 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0555
  time to fit residues: 3.1745
Evaluate side-chains
  32 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 50 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 216 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.046331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.033867 restraints weight = 31610.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.035180 restraints weight = 19235.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.036085 restraints weight = 13821.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.036662 restraints weight = 11063.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.037107 restraints weight = 9608.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.5081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4329  Z= 0.209
  Angle     :  0.632   8.637   5854  Z= 0.332
  Chirality :  0.047   0.332    649
  Planarity :  0.005   0.051    774
  Dihedral  :  4.766  17.098    586
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 17.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  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: -0.30 (0.37), residues: 530
  helix:  0.84 (0.40), residues: 170
  sheet: -1.21 (0.42), residues: 134
  loop : -0.17 (0.45), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 262 
 TYR   0.014   0.002   TYR B 122 
 PHE   0.012   0.002   PHE A  11 
 TRP   0.011   0.002   TRP A 169 
 HIS   0.003   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 4329)
  covalent geometry    : angle       0.63155 ( 5854)
  hydrogen bonds       : bond        0.03682 (  205)
  hydrogen bonds       : angle       5.65074 (  543)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.9553 (ptm) cc_final: 0.9166 (ptm)
REVERT: B   94 GLU cc_start: 0.9215 (pm20) cc_final: 0.8535 (pt0)
REVERT: B  104 MET cc_start: 0.9398 (tpp) cc_final: 0.9188 (tpp)
REVERT: B  194 MET cc_start: 0.9567 (ptm) cc_final: 0.9300 (ptm)
REVERT: B  197 GLN cc_start: 0.9647 (pt0) cc_final: 0.9239 (mp10)
REVERT: B  233 PHE cc_start: 0.8843 (m-80) cc_final: 0.8500 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.0542
  time to fit residues: 2.7923
Evaluate side-chains
  28 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 49 optimal weight:    8.9990
   chunk 48 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0870
   chunk 34 optimal weight:    0.9980
   chunk 25 optimal weight:   10.0000
   overall best weight:    0.9360

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

Flipped N/Q/H residues before XYZ refinement:
** B  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.047367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.034402 restraints weight = 31184.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.035764 restraints weight = 18882.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.036724 restraints weight = 13690.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.037373 restraints weight = 11070.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.037745 restraints weight = 9603.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.5184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4329  Z= 0.112
  Angle     :  0.565   8.548   5854  Z= 0.291
  Chirality :  0.047   0.283    649
  Planarity :  0.004   0.040    774
  Dihedral  :  4.406  18.625    586
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  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: -0.03 (0.38), residues: 530
  helix:  1.06 (0.41), residues: 170
  sheet: -0.80 (0.50), residues: 106
  loop : -0.31 (0.42), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  30 
 TYR   0.011   0.001   TYR B 122 
 PHE   0.015   0.001   PHE A  11 
 TRP   0.006   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 4329)
  covalent geometry    : angle       0.56507 ( 5854)
  hydrogen bonds       : bond        0.03160 (  205)
  hydrogen bonds       : angle       5.41982 (  543)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 782.27 seconds
wall clock time: 14 minutes 11.03 seconds (851.03 seconds total)