Starting phenix.real_space_refine
on Wed Mar  5 14:17:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6x0v_21985/03_2025/6x0v_21985_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x0v_21985/03_2025/6x0v_21985.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6x0v_21985/03_2025/6x0v_21985.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x0v_21985/03_2025/6x0v_21985.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x0v_21985/03_2025/6x0v_21985_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x0v_21985/03_2025/6x0v_21985_neut.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
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
     S       4      5.16       5
     C     814      2.51       5
     N     250      2.21       5
     O     254      1.98       5
     H      62      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 1384
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "E"
      Number of atoms: 227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 227
          Classifications: {'peptide': 46}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 2, 'TRANS': 43}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 127
          Unresolved non-hydrogen angles: 161
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 55
    Chain: "F"
      Number of atoms: 475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 475
          Classifications: {'peptide': 95}
          Incomplete info: {'truncation_to_alanine': 90}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
          Chain breaks: 1
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 324
          Unresolved non-hydrogen angles: 414
          Unresolved non-hydrogen dihedrals: 264
          Unresolved non-hydrogen chiralities: 33
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 169
    Chain: "G"
      Number of atoms: 333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 333
          Classifications: {'peptide': 35}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 34}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "H"
      Number of atoms: 349
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 349
          Classifications: {'peptide': 35}
          Link IDs: {'TRANS': 34}
  Time building chain proxies: 2.29, per 1000 atoms: 1.65
  Number of scatterers: 1384
  At special positions: 0
  Unit cell: (62.16, 60.088, 76.664, 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       4     16.00
     O     254      8.00
     N     250      7.00
     C     814      6.00
     H      62      1.00
    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: 0.37
  Conformation dependent library (CDL) restraints added in 198.2 milliseconds
  

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  416

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 0 sheets defined
      78.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'E' and resid 37 through 49
      removed outlier: 3.610A  pdb=" N   ALA E  47 " --> pdb=" O   LEU E  43 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 52 through 65
      removed outlier: 3.569A  pdb=" N   ASP E  61 " --> pdb=" O   LYS E  57 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LEU E  63 " --> pdb=" O   LEU E  59 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 68 through 79
    Processing helix  chain 'F' and resid 6 through 18
      removed outlier: 3.576A  pdb=" N   LEU F  17 " --> pdb=" O   LEU F  13 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 27 through 32
    Processing helix  chain 'F' and resid 46 through 56
      removed outlier: 3.737A  pdb=" N   LYS F  50 " --> pdb=" O   ALA F  46 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   VAL F  51 " --> pdb=" O   HIS F  47 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ALA F  54 " --> pdb=" O   LYS F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 61 through 73
      removed outlier: 4.347A  pdb=" N   TYR F  67 " --> pdb=" O   PHE F  63 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 77 through 87
    Processing helix  chain 'F' and resid 92 through 103
      removed outlier: 3.747A  pdb=" N   TYR F  97 " --> pdb=" O   GLU F  93 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLN F 100 " --> pdb=" O   GLN F  96 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 61 through 90
      removed outlier: 3.577A  pdb=" N   ASN G  65 " --> pdb=" O   LYS G  61 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ASN G  76 " --> pdb=" O   LYS G  72 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   ARG G  80 " --> pdb=" O   ASN G  76 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE G  81 " --> pdb=" O   LEU G  77 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   PHE G  83 " --> pdb=" O   LEU G  79 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU G  84 " --> pdb=" O   ARG G  80 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   MET G  88 " --> pdb=" O   LEU G  84 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 61 through 91
      removed outlier: 3.686A  pdb=" N   ASN H  65 " --> pdb=" O   LYS H  61 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   ILE H  67 " --> pdb=" O   PHE H  63 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR H  68 " --> pdb=" O   GLU H  64 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   LEU H  77 " --> pdb=" O   GLU H  73 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LYS H  78 " --> pdb=" O   ASN H  74 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ILE H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   TYR H  82 " --> pdb=" O   LYS H  78 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   PHE H  83 " --> pdb=" O   LEU H  79 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   GLU H  86 " --> pdb=" O   TYR H  82 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   MET H  88 " --> pdb=" O   LEU H  84 " (cutoff:3.500A)

    95 hydrogen bonds defined for protein.
    285 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: 0.32

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        0.86 -     1.05: 62
        1.05 -     1.24: 103
        1.24 -     1.43: 440
        1.43 -     1.61: 775
        1.61 -     1.80: 8
  Bond restraints: 1388
  Sorted by residual:
  bond pdb=" N   ILE G  67 "
       pdb=" CA  ILE G  67 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 7.76e+00
  bond pdb=" N   ILE G  67 "
       pdb=" H   ILE G  67 "
    ideal  model  delta    sigma   weight residual
    0.860  0.911 -0.051 2.00e-02 2.50e+03 6.51e+00
  bond pdb=" N   GLU G  69 "
       pdb=" H   GLU G  69 "
    ideal  model  delta    sigma   weight residual
    0.860  0.911 -0.051 2.00e-02 2.50e+03 6.50e+00
  bond pdb=" N   THR G  68 "
       pdb=" H   THR G  68 "
    ideal  model  delta    sigma   weight residual
    0.860  0.911 -0.051 2.00e-02 2.50e+03 6.46e+00
  bond pdb=" N   ASN G  65 "
       pdb=" H   ASN G  65 "
    ideal  model  delta    sigma   weight residual
    0.860  0.911 -0.051 2.00e-02 2.50e+03 6.44e+00
  ... (remaining 1383 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 1829
        1.29 -     2.58: 64
        2.58 -     3.87: 23
        3.87 -     5.16: 8
        5.16 -     6.46: 1
  Bond angle restraints: 1925
  Sorted by residual:
  angle pdb=" C   THR G  68 "
        pdb=" CA  THR G  68 "
        pdb=" CB  THR G  68 "
      ideal   model   delta    sigma   weight residual
     110.85  117.31   -6.46 1.70e+00 3.46e-01 1.44e+01
  angle pdb=" CA  ILE H  67 "
        pdb=" C   ILE H  67 "
        pdb=" O   ILE H  67 "
      ideal   model   delta    sigma   weight residual
     121.27  117.36    3.91 1.04e+00 9.25e-01 1.41e+01
  angle pdb=" C   THR G  68 "
        pdb=" N   GLU G  69 "
        pdb=" CA  GLU G  69 "
      ideal   model   delta    sigma   weight residual
     120.28  125.28   -5.00 1.34e+00 5.57e-01 1.39e+01
  angle pdb=" C   GLU G  64 "
        pdb=" N   ASN G  65 "
        pdb=" CA  ASN G  65 "
      ideal   model   delta    sigma   weight residual
     120.28  124.90   -4.62 1.34e+00 5.57e-01 1.19e+01
  angle pdb=" C   ASP G  62 "
        pdb=" N   PHE G  63 "
        pdb=" CA  PHE G  63 "
      ideal   model   delta    sigma   weight residual
     120.28  124.80   -4.52 1.34e+00 5.57e-01 1.14e+01
  ... (remaining 1920 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.07: 767
       10.07 -    20.15: 56
       20.15 -    30.22: 31
       30.22 -    40.29: 11
       40.29 -    50.37: 3
  Dihedral angle restraints: 868
    sinusoidal: 244
      harmonic: 624
  Sorted by residual:
  dihedral pdb=" C   THR G  68 "
           pdb=" N   THR G  68 "
           pdb=" CA  THR G  68 "
           pdb=" CB  THR G  68 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -132.01   10.01     0      2.50e+00 1.60e-01 1.60e+01
  dihedral pdb=" CA  ARG F  18 "
           pdb=" C   ARG F  18 "
           pdb=" N   VAL F  19 "
           pdb=" CA  VAL F  19 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.76  -19.24     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  GLN G  66 "
           pdb=" CB  GLN G  66 "
           pdb=" CG  GLN G  66 "
           pdb=" CD  GLN G  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.37   50.37     3      1.50e+01 4.44e-03 8.89e+00
  ... (remaining 865 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 178
       0.049 -    0.098: 35
       0.098 -    0.147: 7
       0.147 -    0.196: 1
       0.196 -    0.246: 1
  Chirality restraints: 222
  Sorted by residual:
  chirality pdb=" CA  THR G  68 "
            pdb=" N   THR G  68 "
            pdb=" C   THR G  68 "
            pdb=" CB  THR G  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CA  ILE G  67 "
            pdb=" N   ILE G  67 "
            pdb=" C   ILE G  67 "
            pdb=" CB  ILE G  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.14e-01
  chirality pdb=" CA  ILE H  67 "
            pdb=" N   ILE H  67 "
            pdb=" C   ILE H  67 "
            pdb=" CB  ILE H  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.58e-01
  ... (remaining 219 not shown)

  Planarity restraints: 309
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS G  61 "   -0.025 2.00e-02 2.50e+03   4.86e-02 2.36e+01
        pdb=" C   LYS G  61 "    0.084 2.00e-02 2.50e+03
        pdb=" O   LYS G  61 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   ASP G  62 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS G  61 "   -0.013 2.00e-02 2.50e+03   2.43e-02 5.89e+00
        pdb=" N   ASP G  62 "    0.042 2.00e-02 2.50e+03
        pdb=" CA  ASP G  62 "   -0.011 2.00e-02 2.50e+03
        pdb=" H   ASP G  62 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE H  67 "    0.007 2.00e-02 2.50e+03   1.49e-02 2.23e+00
        pdb=" C   ILE H  67 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ILE H  67 "    0.010 2.00e-02 2.50e+03
        pdb=" N   THR H  68 "    0.009 2.00e-02 2.50e+03
  ... (remaining 306 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 9
        2.28 -     2.86: 830
        2.86 -     3.44: 2029
        3.44 -     4.02: 2255
        4.02 -     4.60: 3249
  Nonbonded interactions: 8372
  Sorted by model distance:
  nonbonded pdb=" O   ASN G  74 "
            pdb=" H   LEU G  77 "
     model   vdw
     1.705 2.450
  nonbonded pdb=" OE1 GLU H  64 "
            pdb=" H   GLU H  64 "
     model   vdw
     1.733 2.450
  nonbonded pdb=" O   LYS H  71 "
            pdb=" H   ASN H  74 "
     model   vdw
     1.775 2.450
  nonbonded pdb=" O   GLU H  86 "
            pdb=" H   GLN H  89 "
     model   vdw
     1.817 2.450
  nonbonded pdb=" O   LYS G  78 "
            pdb=" H   ILE G  81 "
     model   vdw
     1.939 2.450
  ... (remaining 8367 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 'G' and resid 58 through 90)
  selection = (chain 'H' and (resid 58 through 89 or (resid 90 and (name N or name CA or name  \ 
C or name O or name CB or name H ))))
}

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:             2.170
  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:             0.050
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     10.070
  Find NCS groups from input model:        0.030
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
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   0.033   1326  Z= 0.211
  Angle     :  0.623   6.456   1801  Z= 0.469
  Chirality :  0.043   0.246    222
  Planarity :  0.003   0.049    247
  Dihedral  : 11.582  50.367    394
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 15.16
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  3.48 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 14.93 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.48 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.54), residues: 201
  helix: -1.02 (0.42), residues: 145
  sheet:  None (None), residues: 0
  loop : -2.95 (0.56), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE G  83 
 TYR   0.004   0.001   TYR G  82 
 ARG   0.001   0.000   ARG H  87 

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

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

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Evaluate side-chains
  20 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.160 
Fit side-chains
REVERT: G   64 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.5829 (tm-30)
  outliers start: 3
  outliers final: 1
  residues processed: 20
  average time/residue: 0.1407
  time to fit residues: 3.3372
Evaluate side-chains
  18 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 16
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 7 optimal weight:   20.0000
   chunk 4 optimal weight:   20.0000
   chunk 9 optimal weight:   30.0000
   chunk 5 optimal weight:   20.0000
   chunk 11 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** G  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.124093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.116436 restraints weight = 42284.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.117489 restraints weight = 31243.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.117341 restraints weight = 27664.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   1326  Z= 0.136
  Angle     :  0.402   3.582   1801  Z= 0.236
  Chirality :  0.035   0.126    222
  Planarity :  0.002   0.010    247
  Dihedral  :  3.686  13.080    214
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 16.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.61), residues: 201
  helix:  0.80 (0.44), residues: 157
  sheet:  None (None), residues: 0
  loop : -2.92 (0.66), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.003   0.001   PHE G  83 
 TYR   0.007   0.001   TYR H  82 
 ARG   0.002   0.000   ARG H  80 

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

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

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Evaluate side-chains
  24 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.132 
Fit side-chains
REVERT: H   60 MET cc_start: 0.8580 (tmm) cc_final: 0.8204 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.1171
  time to fit residues: 3.3687
Evaluate side-chains
  20 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 12 optimal weight:   20.0000
   chunk 8 optimal weight:    0.9980
   chunk 1 optimal weight:   20.0000
   chunk 11 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0470
   chunk 9 optimal weight:   30.0000
   chunk 16 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    2.2082

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

Flipped N/Q/H residues before XYZ refinement:
H  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.121913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.115482 restraints weight = 41819.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.115990 restraints weight = 34129.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.116212 restraints weight = 28555.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.3413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   1326  Z= 0.178
  Angle     :  0.446   3.985   1801  Z= 0.258
  Chirality :  0.037   0.134    222
  Planarity :  0.002   0.010    247
  Dihedral  :  3.859  17.214    214
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 16.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.96 %
    Favored  : 91.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.63), residues: 201
  helix:  1.48 (0.45), residues: 158
  sheet:  None (None), residues: 0
  loop : -2.77 (0.71), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.011   0.001   PHE G  83 
 TYR   0.005   0.001   TYR H  82 
 ARG   0.002   0.000   ARG H  87 

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

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

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Evaluate side-chains
  21 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.161 
Fit side-chains
REVERT: H   60 MET cc_start: 0.8584 (tmm) cc_final: 0.8359 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0884
  time to fit residues: 2.3447
Evaluate side-chains
  18 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 13 optimal weight:    0.8980
   chunk 7 optimal weight:   30.0000
   chunk 15 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 4 optimal weight:   20.0000
   chunk 6 optimal weight:    0.8980
   chunk 3 optimal weight:   20.0000
   chunk 10 optimal weight:    0.0870
   overall best weight:    0.7760

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

Flipped N/Q/H residues before XYZ refinement:
** G  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.127474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.119852 restraints weight = 40612.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.120055 restraints weight = 32052.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.120232 restraints weight = 28267.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.3861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   1326  Z= 0.100
  Angle     :  0.337   2.605   1801  Z= 0.203
  Chirality :  0.035   0.129    222
  Planarity :  0.001   0.007    247
  Dihedral  :  3.303  11.110    214
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 19.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.65), residues: 201
  helix:  2.27 (0.46), residues: 159
  sheet:  None (None), residues: 0
  loop : -2.80 (0.72), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.005   0.001   PHE H  63 
 TYR   0.007   0.001   TYR H  82 
 ARG   0.001   0.000   ARG H  87 

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

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

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Evaluate side-chains
  21 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.161 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0910
  time to fit residues: 2.4122
Evaluate side-chains
  19 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 4 optimal weight:   20.0000
   chunk 18 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 8 optimal weight:   30.0000
   chunk 1 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 9 optimal weight:   30.0000
   chunk 17 optimal weight:    1.9990
   chunk 2 optimal weight:   20.0000
   chunk 10 optimal weight:   20.0000
   chunk 13 optimal weight:    0.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
G  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.121963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.114231 restraints weight = 41804.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.115789 restraints weight = 31754.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.114952 restraints weight = 28354.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.3761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   1326  Z= 0.226
  Angle     :  0.476   4.685   1801  Z= 0.273
  Chirality :  0.037   0.135    222
  Planarity :  0.002   0.012    247
  Dihedral  :  3.923  18.660    214
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 17.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.63), residues: 201
  helix:  1.89 (0.45), residues: 156
  sheet:  None (None), residues: 0
  loop : -2.78 (0.73), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.002   PHE G  83 
 TYR   0.007   0.001   TYR H  82 
 ARG   0.002   0.000   ARG H  87 

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

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

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Evaluate side-chains
  22 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.160 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.1108
  time to fit residues: 2.9367
Evaluate side-chains
  19 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 10 optimal weight:   30.0000
   chunk 15 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   chunk 7 optimal weight:    9.9990
   chunk 5 optimal weight:    0.8980
   chunk 3 optimal weight:   20.0000
   chunk 12 optimal weight:   20.0000
   chunk 9 optimal weight:    6.9990
   chunk 1 optimal weight:   20.0000
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** G  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.124240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.116255 restraints weight = 43095.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.116616 restraints weight = 31501.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.116505 restraints weight = 29474.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.4041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   1326  Z= 0.120
  Angle     :  0.349   2.360   1801  Z= 0.209
  Chirality :  0.035   0.127    222
  Planarity :  0.001   0.007    247
  Dihedral  :  3.374  13.354    214
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 17.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.64), residues: 201
  helix:  2.57 (0.45), residues: 153
  sheet:  None (None), residues: 0
  loop : -2.85 (0.69), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.001   PHE G  83 
 TYR   0.003   0.001   TYR H  82 
 ARG   0.001   0.000   ARG H  87 

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

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

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Evaluate side-chains
  22 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.176 
Fit side-chains
REVERT: G   62 ASP cc_start: 0.8133 (p0) cc_final: 0.7923 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.0956
  time to fit residues: 2.6270
Evaluate side-chains
  19 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 7 optimal weight:   30.0000
   chunk 13 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0970
   chunk 15 optimal weight:    0.7980
   chunk 11 optimal weight:   20.0000
   chunk 18 optimal weight:    0.9980
   chunk 8 optimal weight:   30.0000
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
** G  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.129206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.121285 restraints weight = 39242.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.122924 restraints weight = 28481.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.122145 restraints weight = 24136.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.4349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.026   1326  Z= 0.106
  Angle     :  0.317   3.048   1801  Z= 0.193
  Chirality :  0.034   0.127    222
  Planarity :  0.001   0.006    247
  Dihedral  :  2.994  10.300    214
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.92 (0.65), residues: 201
  helix:  3.25 (0.45), residues: 154
  sheet:  None (None), residues: 0
  loop : -3.02 (0.69), residues: 47

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.003   0.001   PHE H  83 
 TYR   0.006   0.001   TYR H  82 
 ARG   0.001   0.000   ARG H  87 

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

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

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Evaluate side-chains
  22 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.157 
Fit side-chains
REVERT: G   62 ASP cc_start: 0.8006 (p0) cc_final: 0.7715 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.0859
  time to fit residues: 2.3902
Evaluate side-chains
  19 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 12 optimal weight:   40.0000
   chunk 18 optimal weight:    0.4980
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 1 optimal weight:   20.0000
   chunk 11 optimal weight:    8.9990
   chunk 9 optimal weight:   30.0000
   chunk 16 optimal weight:    0.8980
   chunk 4 optimal weight:   20.0000
   chunk 13 optimal weight:    0.9990
   chunk 2 optimal weight:    7.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
G  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.127074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.118905 restraints weight = 41369.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.120003 restraints weight = 31572.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.119540 restraints weight = 27541.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.4405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   1326  Z= 0.124
  Angle     :  0.347   2.838   1801  Z= 0.209
  Chirality :  0.035   0.129    222
  Planarity :  0.001   0.006    247
  Dihedral  :  3.064  12.507    214
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.84 (0.65), residues: 201
  helix:  3.13 (0.44), residues: 155
  sheet:  None (None), residues: 0
  loop : -2.95 (0.71), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.001   PHE G  75 
 TYR   0.002   0.000   TYR H  82 
 ARG   0.001   0.000   ARG H  87 

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

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

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Evaluate side-chains
  21 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.152 
Fit side-chains
REVERT: G   62 ASP cc_start: 0.8048 (p0) cc_final: 0.7825 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0851
  time to fit residues: 2.2830
Evaluate side-chains
  20 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 4 optimal weight:   20.0000
   chunk 15 optimal weight:    0.8980
   chunk 6 optimal weight:   10.0000
   chunk 1 optimal weight:   30.0000
   chunk 2 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 10 optimal weight:   30.0000
   chunk 17 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
G  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.123506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.116108 restraints weight = 41848.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.116505 restraints weight = 30841.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.116733 restraints weight = 26391.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.4271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   1326  Z= 0.160
  Angle     :  0.399   3.458   1801  Z= 0.232
  Chirality :  0.036   0.131    222
  Planarity :  0.002   0.007    247
  Dihedral  :  3.389  15.189    214
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 16.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.70 (0.64), residues: 201
  helix:  2.88 (0.44), residues: 157
  sheet:  None (None), residues: 0
  loop : -2.63 (0.76), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.007   0.001   PHE G  75 
 TYR   0.004   0.001   TYR H  82 
 ARG   0.001   0.000   ARG G  87 

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

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

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Evaluate side-chains
  21 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.161 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0869
  time to fit residues: 2.3189
Evaluate side-chains
  19 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 7 optimal weight:   30.0000
   chunk 18 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 3 optimal weight:    4.9990
   chunk 2 optimal weight:   20.0000
   chunk 4 optimal weight:   10.0000
   chunk 15 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 8 optimal weight:   30.0000
   chunk 1 optimal weight:    5.9990
   overall best weight:    3.1586

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

Flipped N/Q/H residues before XYZ refinement:
G  74 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.119351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.111715 restraints weight = 44690.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.112615 restraints weight = 34568.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.111977 restraints weight = 30453.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.4254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   1326  Z= 0.248
  Angle     :  0.513   5.388   1801  Z= 0.287
  Chirality :  0.038   0.136    222
  Planarity :  0.002   0.009    247
  Dihedral  :  4.005  17.903    214
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 18.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.62), residues: 201
  helix:  2.27 (0.43), residues: 157
  sheet:  None (None), residues: 0
  loop : -2.70 (0.81), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.009   0.002   PHE G  83 
 TYR   0.008   0.001   TYR H  82 
 ARG   0.001   0.000   ARG G  58 

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

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

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  402 Ramachandran restraints generated.
    201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Residue LYS   61 is missing expected H atoms. Skipping.
Residue ILE   67 is missing expected H atoms. Skipping.
Residue THR   68 is missing expected H atoms. Skipping.
Residue LEU   70 is missing expected H atoms. Skipping.
Residue LYS   71 is missing expected H atoms. Skipping.
Residue LYS   72 is missing expected H atoms. Skipping.
Residue LEU   77 is missing expected H atoms. Skipping.
Residue LYS   78 is missing expected H atoms. Skipping.
Residue LEU   79 is missing expected H atoms. Skipping.
Residue ILE   81 is missing expected H atoms. Skipping.
Residue TYR   82 is missing expected H atoms. Skipping.
Residue LEU   84 is missing expected H atoms. Skipping.
Residue MET   88 is missing expected H atoms. Skipping.
Evaluate side-chains
  20 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.161 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0881
  time to fit residues: 2.2228
Evaluate side-chains
  18 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 19
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 12 optimal weight:   50.0000
   chunk 6 optimal weight:   20.0000
   chunk 3 optimal weight:   20.0000
   chunk 9 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 1 optimal weight:    0.0570
   chunk 18 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
** G  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.127087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.120159 restraints weight = 40065.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.121120 restraints weight = 29464.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.121116 restraints weight = 24006.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.4622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.016   1326  Z= 0.091
  Angle     :  0.308   2.341   1801  Z= 0.190
  Chirality :  0.034   0.125    222
  Planarity :  0.001   0.006    247
  Dihedral  :  3.016  11.323    214
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 14.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.09 (0.65), residues: 201
  helix:  3.27 (0.44), residues: 156
  sheet:  None (None), residues: 0
  loop : -2.82 (0.77), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.003   0.001   PHE G  63 
 TYR   0.004   0.001   TYR H  82 
 ARG   0.001   0.000   ARG G  80 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 781.79 seconds
wall clock time: 14 minutes 15.95 seconds (855.95 seconds total)