Starting phenix.real_space_refine
on Mon Feb 10 19:27:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6x0v_21985/02_2025/6x0v_21985_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x0v_21985/02_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_21985/02_2025/6x0v_21985.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x0v_21985/02_2025/6x0v_21985.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x0v_21985/02_2025/6x0v_21985_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x0v_21985/02_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-5592/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: 2.71, per 1000 atoms: 1.96
  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: 0.43
  Conformation dependent library (CDL) restraints added in 245.2 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: 0.16
  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: 0.41

  Time building geometry restraints manager: 0.49 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:             2.250
  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:             0.040
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     11.250
  Find NCS groups from input model:        0.040
  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:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.710
-------------------------------------------------------------------------------
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  : 0.171 
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: 0.1440
  time to fit residues: 3.3444
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  : 0.167 
-------------------------------------------------------------------------------
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 = 0.116435 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 = 31247.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.117339 restraints weight = 27653.519|
|-----------------------------------------------------------------------------|
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  : 0.170 
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: 0.1214
  time to fit residues: 3.4545
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  : 0.165 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 9 optimal weight:   30.0000
   chunk 16 optimal weight:    4.9990
   chunk 4 optimal weight:   20.0000
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    8.9990
   overall best weight:    1.9784

-------------------------------------------------------------------------------
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 = 0.3591 r_free = 0.3591 target = 0.122893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.116242 restraints weight = 41647.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.116623 restraints weight = 32785.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.117071 restraints weight = 28782.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.3366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   1326  Z= 0.164
  Angle     :  0.422   3.499   1801  Z= 0.245
  Chirality :  0.036   0.132    222
  Planarity :  0.002   0.009    247
  Dihedral  :  3.711  16.080    214
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 16.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  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:  0.98 (0.64), residues: 201
  helix:  1.53 (0.45), residues: 159
  sheet:  None (None), residues: 0
  loop : -2.89 (0.71), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.010   0.001   PHE G  83 
 TYR   0.004   0.001   TYR H  82 
 ARG   0.001   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  : 0.171 
Fit side-chains
REVERT: H   60 MET cc_start: 0.8577 (tmm) cc_final: 0.8338 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0975
  time to fit residues: 2.5710
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  : 0.174 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 7 optimal weight:   30.0000
   chunk 15 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 4 optimal weight:   20.0000
   chunk 6 optimal weight:    5.9990
   chunk 3 optimal weight:   20.0000
   chunk 10 optimal weight:   30.0000
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.3600 r_free = 0.3600 target = 0.123291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.115808 restraints weight = 41346.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.116052 restraints weight = 32488.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.116284 restraints weight = 28249.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.3632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   1326  Z= 0.159
  Angle     :  0.425   3.804   1801  Z= 0.243
  Chirality :  0.036   0.131    222
  Planarity :  0.002   0.007    247
  Dihedral  :  3.731  16.050    214
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 18.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  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:  1.38 (0.64), residues: 201
  helix:  1.84 (0.45), residues: 158
  sheet:  None (None), residues: 0
  loop : -2.74 (0.71), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.005   0.001   PHE G  75 
 TYR   0.010   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  : 0.171 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0938
  time to fit residues: 2.4911
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  : 0.169 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 8 optimal weight:   30.0000
   chunk 1 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 9 optimal weight:   30.0000
   chunk 17 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 10 optimal weight:   20.0000
   chunk 13 optimal weight:    0.6980
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.3628 r_free = 0.3628 target = 0.125535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.117955 restraints weight = 41114.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.119225 restraints weight = 30213.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.118447 restraints weight = 30253.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.3896

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= 0.126
  Angle     :  0.359   2.322   1801  Z= 0.216
  Chirality :  0.036   0.130    222
  Planarity :  0.002   0.006    247
  Dihedral  :  3.401  13.525    214
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 17.39
  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:  1.88 (0.65), residues: 201
  helix:  2.22 (0.46), residues: 158
  sheet:  None (None), residues: 0
  loop : -2.72 (0.74), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.011   0.001   PHE G  83 
 TYR   0.004   0.001   TYR H  82 
 ARG   0.001   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
  23 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.171 
Fit side-chains
REVERT: G   62 ASP cc_start: 0.8097 (p0) cc_final: 0.7887 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.1128
  time to fit residues: 3.1270
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  : 0.168 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 11 optimal weight:   20.0000
   chunk 8 optimal weight:   30.0000
   chunk 7 optimal weight:   20.0000
   chunk 5 optimal weight:   20.0000
   chunk 3 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 1 optimal weight:   20.0000
   overall best weight:    3.1386

-------------------------------------------------------------------------------
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 = 0.3557 r_free = 0.3557 target = 0.119815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.112674 restraints weight = 44213.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.113615 restraints weight = 34801.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.113007 restraints weight = 28021.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.3870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   1326  Z= 0.245
  Angle     :  0.503   5.105   1801  Z= 0.281
  Chirality :  0.038   0.136    222
  Planarity :  0.002   0.012    247
  Dihedral  :  4.009  18.487    214
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 19.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  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:  1.20 (0.63), residues: 201
  helix:  1.76 (0.44), residues: 156
  sheet:  None (None), residues: 0
  loop : -2.81 (0.76), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.011   0.002   PHE G  83 
 TYR   0.006   0.001   TYR H  82 
 ARG   0.002   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  : 0.144 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.0926
  time to fit residues: 2.5579
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  : 0.163 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:   30.0000
   chunk 7 optimal weight:   30.0000
   chunk 13 optimal weight:    0.9980
   chunk 5 optimal weight:   30.0000
   chunk 15 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 8 optimal weight:   30.0000
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.3620 r_free = 0.3620 target = 0.125075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.117602 restraints weight = 39732.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.118756 restraints weight = 28322.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.118136 restraints weight = 24143.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.4170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   1326  Z= 0.124
  Angle     :  0.349   2.606   1801  Z= 0.209
  Chirality :  0.035   0.129    222
  Planarity :  0.001   0.007    247
  Dihedral  :  3.389  12.875    214
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 18.72
  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:  2.13 (0.64), residues: 201
  helix:  2.62 (0.45), residues: 153
  sheet:  None (None), residues: 0
  loop : -2.91 (0.70), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE G  63 
 TYR   0.005   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  : 0.172 
Fit side-chains
REVERT: G   62 ASP cc_start: 0.8183 (p0) cc_final: 0.7925 (p0)
REVERT: G   89 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8156 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.0898
  time to fit residues: 2.4909
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  : 0.170 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 1 optimal weight:   20.0000
   chunk 11 optimal weight:    8.9990
   chunk 9 optimal weight:   30.0000
   chunk 16 optimal weight:    0.6980
   chunk 4 optimal weight:   20.0000
   chunk 13 optimal weight:    0.9990
   chunk 2 optimal weight:   20.0000
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 = 0.3610 r_free = 0.3610 target = 0.124020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.115889 restraints weight = 41698.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.116544 restraints weight = 31247.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.117005 restraints weight = 29294.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.4208

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= 0.151
  Angle     :  0.384   2.903   1801  Z= 0.227
  Chirality :  0.036   0.131    222
  Planarity :  0.002   0.006    247
  Dihedral  :  3.431  14.657    214
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 19.17
  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:  2.33 (0.64), residues: 201
  helix:  2.61 (0.45), residues: 157
  sheet:  None (None), residues: 0
  loop : -2.71 (0.75), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.001   PHE G  75 
 TYR   0.005   0.001   TYR H  82 
 ARG   0.001   0.000   ARG G  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
  22 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.171 
Fit side-chains
REVERT: G   62 ASP cc_start: 0.8235 (p0) cc_final: 0.8014 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.0881
  time to fit residues: 2.4504
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  : 0.168 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 1 optimal weight:   20.0000
   chunk 2 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 10 optimal weight:   20.0000
   chunk 17 optimal weight:    0.9990
   chunk 12 optimal weight:   50.0000
   chunk 11 optimal weight:   20.0000
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.3533 r_free = 0.3533 target = 0.117686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.110496 restraints weight = 43410.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.111243 restraints weight = 33360.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.111060 restraints weight = 27333.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.4045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   1326  Z= 0.326
  Angle     :  0.622   6.765   1801  Z= 0.338
  Chirality :  0.040   0.140    222
  Planarity :  0.003   0.014    247
  Dihedral  :  4.523  20.282    214
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 20.51
  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:  0.73 (0.60), residues: 201
  helix:  1.36 (0.42), residues: 157
  sheet:  None (None), residues: 0
  loop : -2.80 (0.83), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.011   0.002   PHE G  83 
 TYR   0.013   0.002   TYR H  82 
 ARG   0.002   0.001   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
  23 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.156 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0868
  time to fit residues: 2.5108
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  : 0.167 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 7 optimal weight:   30.0000
   chunk 18 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 3 optimal weight:   20.0000
   chunk 2 optimal weight:   20.0000
   chunk 4 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 8 optimal weight:   30.0000
   chunk 1 optimal weight:    3.9990
   overall best weight:    2.5588

-------------------------------------------------------------------------------
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 = 0.3561 r_free = 0.3561 target = 0.120230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.112354 restraints weight = 44484.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.113224 restraints weight = 34444.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.112839 restraints weight = 30404.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.4210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   1326  Z= 0.204
  Angle     :  0.457   4.136   1801  Z= 0.261
  Chirality :  0.037   0.133    222
  Planarity :  0.002   0.007    247
  Dihedral  :  3.972  17.762    214
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 19.17
  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:  1.26 (0.62), residues: 201
  helix:  1.76 (0.43), residues: 157
  sheet:  None (None), residues: 0
  loop : -2.72 (0.82), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.001   PHE G  83 
 TYR   0.006   0.001   TYR H  82 
 ARG   0.001   0.000   ARG H  87 

********************** 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
  22 residues out of total 197 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.175 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.0913
  time to fit residues: 2.5370
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  : 0.172 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 12 optimal weight:   50.0000
   chunk 6 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 1 optimal weight:    0.1980
   chunk 18 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3615 r_free = 0.3615 target = 0.124786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 124)---------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.119952 restraints weight = 3797.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.119335 restraints weight = 6411.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.119331 restraints weight = 6112.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.4431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   1326  Z= 0.103
  Angle     :  0.326   2.056   1801  Z= 0.197
  Chirality :  0.035   0.128    222
  Planarity :  0.001   0.006    247
  Dihedral  :  3.199  11.982    214
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 17.39
  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:  2.56 (0.65), residues: 201
  helix:  2.84 (0.45), residues: 155
  sheet:  None (None), residues: 0
  loop : -2.65 (0.83), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE G  63 
 TYR   0.004   0.001   TYR H  82 
 ARG   0.001   0.000   ARG G  58 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 769.66 seconds
wall clock time: 14 minutes 31.98 seconds (871.98 seconds total)