Starting phenix.real_space_refine
on Wed Sep 17 04:05:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y3n_38892/09_2025/8y3n_38892.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y3n_38892/09_2025/8y3n_38892.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y3n_38892/09_2025/8y3n_38892.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y3n_38892/09_2025/8y3n_38892.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y3n_38892/09_2025/8y3n_38892.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y3n_38892/09_2025/8y3n_38892.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    2321      2.51       5
     N     633      2.21       5
     O     724      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3694
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 917
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 6, 'TRANS': 116}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 939
          Classifications: {'peptide': 125}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 118}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 925
          Classifications: {'peptide': 123}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 116}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 913
          Classifications: {'peptide': 123}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 116}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 1.35, per 1000 atoms: 0.37
  Number of scatterers: 3694
  At special positions: 0
  Unit cell: (70.3, 94.05, 86.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      16     16.00
     O     724      8.00
     N     633      7.00
     C    2321      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.23
  Conformation dependent library (CDL) restraints added in 131.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  932

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 5 sheets defined
      20.9% alpha, 42.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 97 through 113
      removed outlier: 3.566A  pdb=" N   CYS A 101 " --> pdb=" O   THR A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 124
      removed outlier: 3.620A  pdb=" N   SER A 120 " --> pdb=" O   ASN A 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 112
      removed outlier: 3.500A  pdb=" N   LEU B 112 " --> pdb=" O   MET B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 124
    Processing helix  chain 'C' and resid 97 through 112
      removed outlier: 3.771A  pdb=" N   CYS C 101 " --> pdb=" O   THR C  97 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 116 through 125
    Processing helix  chain 'D' and resid 97 through 112
    Processing helix  chain 'D' and resid 116 through 125
    Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8
      removed outlier: 3.547A  pdb=" N   PHE A   7 " --> pdb=" O   VAL A  20 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL A  20 " --> pdb=" O   PHE A   7 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   ILE A  33 " --> pdb=" O   PRO A  22 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ALA A  26 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL A  64 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   SER A  84 " --> pdb=" O   VAL A  64 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   TRP A  82 " --> pdb=" O   LYS A  66 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 8
      removed outlier: 3.547A  pdb=" N   PHE A   7 " --> pdb=" O   VAL A  20 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL A  20 " --> pdb=" O   PHE A   7 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   ILE A  33 " --> pdb=" O   PRO A  22 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ALA A  26 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   LEU A  90 " --> pdb=" O   TYR A  58 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE A  60 " --> pdb=" O   MET A  88 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL A  62 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   GLU B  89 " --> pdb=" O   ASN A  87 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   GLU A  89 " --> pdb=" O   ASN B  87 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ASN B  87 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
      removed outlier: 8.551A  pdb=" N   ARG B  83 " --> pdb=" O   PRO A  93 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ALA B  80 " --> pdb=" O   ALA B  68 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   ALA B  68 " --> pdb=" O   ALA B  80 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   TRP B  82 " --> pdb=" O   LYS B  66 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LYS B  66 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   VAL B  64 " --> pdb=" O   SER B  84 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   VAL B  62 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ALA B  46 " --> pdb=" O   ALA B  30 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   VAL B  29 " --> pdb=" O   PHE B  25 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   PHE B  25 " --> pdb=" O   VAL B  29 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   GLU B  31 " --> pdb=" O   SER B  23 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   VAL B  18 " --> pdb=" O   LEU B   9 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 7 through 10
      removed outlier: 6.736A  pdb=" N   VAL C  18 " --> pdb=" O   LEU C   9 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   GLU C  31 " --> pdb=" O   SER C  23 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   PHE C  25 " --> pdb=" O   VAL C  29 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   VAL C  29 " --> pdb=" O   PHE C  25 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   ALA C  46 " --> pdb=" O   ALA C  30 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   THR C  59 " --> pdb=" O   SER C  47 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   VAL C  64 " --> pdb=" O   SER C  84 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER C  84 " --> pdb=" O   VAL C  64 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   TRP C  82 " --> pdb=" O   LYS C  66 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 7 through 10
      removed outlier: 6.736A  pdb=" N   VAL C  18 " --> pdb=" O   LEU C   9 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   GLU C  31 " --> pdb=" O   SER C  23 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   PHE C  25 " --> pdb=" O   VAL C  29 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   VAL C  29 " --> pdb=" O   PHE C  25 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   ALA C  46 " --> pdb=" O   ALA C  30 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   THR C  59 " --> pdb=" O   SER C  47 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU D  89 " --> pdb=" O   ASN C  87 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLU C  89 " --> pdb=" O   ASN D  87 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 21 through 26
      removed outlier: 7.003A  pdb=" N   GLU D  31 " --> pdb=" O   SER D  23 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   PHE D  25 " --> pdb=" O   VAL D  29 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   VAL D  29 " --> pdb=" O   PHE D  25 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA D  46 " --> pdb=" O   ALA D  30 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL D  44 " --> pdb=" O   TRP D  32 " (cutoff:3.500A)

    179 hydrogen bonds defined for protein.
    492 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: 0.48

  Time building geometry restraints manager: 0.33 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1203
        1.34 -     1.45: 534
        1.45 -     1.57: 1995
        1.57 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 3756
  Sorted by residual:
  bond pdb=" CG  ASN A  12 "
       pdb=" OD1 ASN A  12 "
    ideal  model  delta    sigma   weight residual
    1.231  1.328 -0.097 1.90e-02 2.77e+03 2.63e+01
  bond pdb=" CG  ASN D  87 "
       pdb=" OD1 ASN D  87 "
    ideal  model  delta    sigma   weight residual
    1.231  1.326 -0.095 1.90e-02 2.77e+03 2.50e+01
  bond pdb=" CG  ASN C 116 "
       pdb=" ND2 ASN C 116 "
    ideal  model  delta    sigma   weight residual
    1.328  1.227  0.101 2.10e-02 2.27e+03 2.30e+01
  bond pdb=" CG  ASN D  87 "
       pdb=" ND2 ASN D  87 "
    ideal  model  delta    sigma   weight residual
    1.328  1.230  0.098 2.10e-02 2.27e+03 2.17e+01
  bond pdb=" CG  ASN A  12 "
       pdb=" ND2 ASN A  12 "
    ideal  model  delta    sigma   weight residual
    1.328  1.230  0.098 2.10e-02 2.27e+03 2.16e+01
  ... (remaining 3751 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 4729
        1.34 -     2.69: 298
        2.69 -     4.03: 59
        4.03 -     5.38: 24
        5.38 -     6.72: 7
  Bond angle restraints: 5117
  Sorted by residual:
  angle pdb=" C   MET A 108 "
        pdb=" N   GLN A 109 "
        pdb=" CA  GLN A 109 "
      ideal   model   delta    sigma   weight residual
     120.28  115.24    5.04 1.34e+00 5.57e-01 1.41e+01
  angle pdb=" N   GLU D  31 "
        pdb=" CA  GLU D  31 "
        pdb=" C   GLU D  31 "
      ideal   model   delta    sigma   weight residual
     107.49  113.99   -6.50 1.74e+00 3.30e-01 1.40e+01
  angle pdb=" N   GLU B 102 "
        pdb=" CA  GLU B 102 "
        pdb=" C   GLU B 102 "
      ideal   model   delta    sigma   weight residual
     111.28  107.34    3.94 1.09e+00 8.42e-01 1.31e+01
  angle pdb=" CB  ASN C 116 "
        pdb=" CG  ASN C 116 "
        pdb=" ND2 ASN C 116 "
      ideal   model   delta    sigma   weight residual
     116.40  121.36   -4.96 1.50e+00 4.44e-01 1.09e+01
  angle pdb=" CA  GLN C  54 "
        pdb=" CB  GLN C  54 "
        pdb=" CG  GLN C  54 "
      ideal   model   delta    sigma   weight residual
     114.10  120.38   -6.28 2.00e+00 2.50e-01 9.87e+00
  ... (remaining 5112 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.07: 2001
       14.07 -    28.13: 188
       28.13 -    42.20: 59
       42.20 -    56.27: 14
       56.27 -    70.33: 3
  Dihedral angle restraints: 2265
    sinusoidal: 833
      harmonic: 1432
  Sorted by residual:
  dihedral pdb=" CA  SER D  52 "
           pdb=" C   SER D  52 "
           pdb=" N   ALA D  53 "
           pdb=" CA  ALA D  53 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.74  -19.26     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  GLN C  50 "
           pdb=" C   GLN C  50 "
           pdb=" N   SER C  51 "
           pdb=" CA  SER C  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.06  -18.94     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  SER A 126 "
           pdb=" C   SER A 126 "
           pdb=" N   GLY A 127 "
           pdb=" CA  GLY A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.00  -18.00     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 2262 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 328
       0.032 -    0.063: 173
       0.063 -    0.094: 63
       0.094 -    0.126: 39
       0.126 -    0.157: 7
  Chirality restraints: 610
  Sorted by residual:
  chirality pdb=" CA  PRO C 117 "
            pdb=" N   PRO C 117 "
            pdb=" C   PRO C 117 "
            pdb=" CB  PRO C 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.17e-01
  chirality pdb=" CA  PRO B 117 "
            pdb=" N   PRO B 117 "
            pdb=" C   PRO B 117 "
            pdb=" CB  PRO B 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.02e-01
  chirality pdb=" CA  ILE C  60 "
            pdb=" N   ILE C  60 "
            pdb=" C   ILE C  60 "
            pdb=" CB  ILE C  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.51e-01
  ... (remaining 607 not shown)

  Planarity restraints: 659
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 116 "    0.039 5.00e-02 4.00e+02   5.83e-02 5.44e+00
        pdb=" N   PRO B 117 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO B 117 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 117 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D 107 "    0.009 2.00e-02 2.50e+03   1.88e-02 3.54e+00
        pdb=" C   ALA D 107 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   ALA D 107 "    0.012 2.00e-02 2.50e+03
        pdb=" N   MET D 108 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D 116 "    0.028 5.00e-02 4.00e+02   4.31e-02 2.97e+00
        pdb=" N   PRO D 117 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO D 117 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO D 117 "    0.025 5.00e-02 4.00e+02
  ... (remaining 656 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.89: 1463
        2.89 -     3.39: 3453
        3.39 -     3.89: 5627
        3.89 -     4.40: 5947
        4.40 -     4.90: 10962
  Nonbonded interactions: 27452
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN C  24 "
            pdb=" N   PHE C  25 "
     model   vdw
     2.382 3.120
  nonbonded pdb=" O   TYR D  58 "
            pdb=" OG1 THR D  59 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" NH1 ARG A  56 "
            pdb=" O   ASN B 125 "
     model   vdw
     2.398 3.120
  nonbonded pdb=" ND2 ASN C  12 "
            pdb=" O   GLY C  16 "
     model   vdw
     2.399 3.120
  nonbonded pdb=" NE2 GLN A 109 "
            pdb=" O   LEU B 112 "
     model   vdw
     2.404 3.120
  ... (remaining 27447 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 2 through 112 or (resid 113 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 114 through 128))
  selection = (chain 'B' and (resid 2 through 71 or resid 77 through 112 or (resid 113 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 114 through 128))
  selection = (chain 'C' and (resid 2 through 112 or (resid 113 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 114 through 128))
  selection = (chain 'D' and resid 2 through 128)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.770
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
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      :  0.007   0.101   3756  Z= 0.344
  Angle     :  0.820   6.721   5117  Z= 0.469
  Chirality :  0.048   0.157    610
  Planarity :  0.006   0.058    659
  Dihedral  : 13.357  70.333   1333
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.92 %
    Favored  : 88.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.00 (0.37), residues: 478
  helix:  0.28 (0.52), residues: 101
  sheet: -2.52 (0.38), residues: 159
  loop : -2.64 (0.40), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  83 
 TYR   0.012   0.002   TYR B  42 
 PHE   0.028   0.003   PHE D   4 
 TRP   0.023   0.003   TRP B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00726 ( 3756)
  covalent geometry    : angle       0.82013 ( 5117)
  hydrogen bonds       : bond        0.16791 (  150)
  hydrogen bonds       : angle       7.59665 (  492)

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

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

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.139 
Fit side-chains
REVERT: C   27 ASN cc_start: 0.7206 (t0) cc_final: 0.6970 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.0512
  time to fit residues: 5.2233
Evaluate side-chains
  60 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0980
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
C  87 ASN
D  27 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.151632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.122253 restraints weight = 4538.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.123499 restraints weight = 3807.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.124546 restraints weight = 3407.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.124963 restraints weight = 3169.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.125840 restraints weight = 3036.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3756  Z= 0.139
  Angle     :  0.639   8.941   5117  Z= 0.329
  Chirality :  0.046   0.131    610
  Planarity :  0.005   0.041    659
  Dihedral  :  5.648  50.715    518
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  9.36 %
    Favored  : 89.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.32 (0.38), residues: 478
  helix:  0.72 (0.51), residues: 102
  sheet: -1.97 (0.41), residues: 161
  loop : -2.27 (0.41), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  83 
 TYR   0.008   0.001   TYR B  42 
 PHE   0.018   0.002   PHE D   4 
 TRP   0.016   0.002   TRP A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3756)
  covalent geometry    : angle       0.63855 ( 5117)
  hydrogen bonds       : bond        0.04165 (  150)
  hydrogen bonds       : angle       5.38218 (  492)

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

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

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A   40 GLN cc_start: 0.8695 (tp40) cc_final: 0.8428 (tp-100)
  outliers start: 5
  outliers final: 4
  residues processed: 67
  average time/residue: 0.0520
  time to fit residues: 4.6760
Evaluate side-chains
  57 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain C residue   87 ASN
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain D residue   48 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 37 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 29 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 47 optimal weight:    7.9990
   chunk 44 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
B  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.149587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.120035 restraints weight = 4555.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.121531 restraints weight = 3826.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 16)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.122371 restraints weight = 3416.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.123185 restraints weight = 3165.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.123185 restraints weight = 3011.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3756  Z= 0.187
  Angle     :  0.641   6.757   5117  Z= 0.331
  Chirality :  0.046   0.138    610
  Planarity :  0.005   0.076    659
  Dihedral  :  5.689  54.996    518
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.79 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 12.07 %
    Favored  : 86.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.18 (0.39), residues: 478
  helix:  0.85 (0.50), residues: 101
  sheet: -1.83 (0.42), residues: 166
  loop : -2.21 (0.41), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  56 
 TYR   0.014   0.002   TYR D  85 
 PHE   0.017   0.002   PHE D   4 
 TRP   0.018   0.003   TRP A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 3756)
  covalent geometry    : angle       0.64062 ( 5117)
  hydrogen bonds       : bond        0.04169 (  150)
  hydrogen bonds       : angle       5.06885 (  492)

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

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

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.8841 (pp30) cc_final: 0.8369 (pp30)
REVERT: A   40 GLN cc_start: 0.8731 (tp40) cc_final: 0.8332 (tp-100)
  outliers start: 4
  outliers final: 3
  residues processed: 61
  average time/residue: 0.0505
  time to fit residues: 4.1533
Evaluate side-chains
  57 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain D residue   48 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0010
   chunk 27 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    2.3994

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

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN
B  27 ASN
B  40 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.150070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.120616 restraints weight = 4503.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.121896 restraints weight = 3769.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.123127 restraints weight = 3373.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.123127 restraints weight = 3123.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.123127 restraints weight = 3123.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3756  Z= 0.164
  Angle     :  0.615   7.859   5117  Z= 0.318
  Chirality :  0.045   0.140    610
  Planarity :  0.005   0.074    659
  Dihedral  :  5.672  61.787    518
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 16.75 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.93 (0.39), residues: 478
  helix:  1.17 (0.50), residues: 101
  sheet: -1.65 (0.42), residues: 166
  loop : -2.15 (0.41), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  56 
 TYR   0.014   0.001   TYR D  85 
 PHE   0.015   0.002   PHE D   4 
 TRP   0.017   0.002   TRP A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 3756)
  covalent geometry    : angle       0.61475 ( 5117)
  hydrogen bonds       : bond        0.03842 (  150)
  hydrogen bonds       : angle       4.72766 (  492)

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

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

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.8821 (pp30) cc_final: 0.8376 (pp30)
REVERT: A   40 GLN cc_start: 0.8683 (tp40) cc_final: 0.8458 (tp-100)
REVERT: B   27 ASN cc_start: 0.7904 (m-40) cc_final: 0.7412 (t0)
REVERT: D  125 ASN cc_start: 0.7783 (OUTLIER) cc_final: 0.7376 (m110)
  outliers start: 7
  outliers final: 4
  residues processed: 59
  average time/residue: 0.0455
  time to fit residues: 3.7557
Evaluate side-chains
  54 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  125 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 12 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 7 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 13 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  40 GLN
C  50 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.151520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.121733 restraints weight = 4444.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.123440 restraints weight = 3652.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.124386 restraints weight = 3194.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.125447 restraints weight = 2930.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.125447 restraints weight = 2743.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3756  Z= 0.138
  Angle     :  0.594   7.687   5117  Z= 0.303
  Chirality :  0.045   0.138    610
  Planarity :  0.005   0.074    659
  Dihedral  :  5.625  67.756    518
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 17.98 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.75 (0.39), residues: 478
  helix:  1.26 (0.50), residues: 101
  sheet: -1.46 (0.42), residues: 164
  loop : -2.09 (0.41), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  83 
 TYR   0.012   0.001   TYR D  85 
 PHE   0.012   0.002   PHE C   4 
 TRP   0.015   0.002   TRP A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3756)
  covalent geometry    : angle       0.59369 ( 5117)
  hydrogen bonds       : bond        0.03600 (  150)
  hydrogen bonds       : angle       4.53378 (  492)

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

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

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.8832 (pp30) cc_final: 0.8375 (pp30)
REVERT: B   27 ASN cc_start: 0.7839 (m-40) cc_final: 0.7490 (t0)
REVERT: D  125 ASN cc_start: 0.7614 (OUTLIER) cc_final: 0.7183 (m110)
  outliers start: 9
  outliers final: 5
  residues processed: 63
  average time/residue: 0.0405
  time to fit residues: 3.6371
Evaluate side-chains
  59 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  125 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 43 optimal weight:   10.0000
   chunk 14 optimal weight:    0.0050
   chunk 2 optimal weight:    0.9980
   chunk 41 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 31 optimal weight:    0.6980
   chunk 30 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    1.3396

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.153860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.122309 restraints weight = 4486.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.124717 restraints weight = 3398.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.126292 restraints weight = 2816.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.127482 restraints weight = 2498.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.128111 restraints weight = 2297.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7548
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3756  Z= 0.121
  Angle     :  0.580   8.122   5117  Z= 0.297
  Chirality :  0.044   0.131    610
  Planarity :  0.005   0.077    659
  Dihedral  :  5.607  73.186    518
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 19.21 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.55 (0.39), residues: 478
  helix:  1.37 (0.50), residues: 101
  sheet: -1.34 (0.42), residues: 166
  loop : -1.93 (0.41), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  83 
 TYR   0.013   0.001   TYR D  85 
 PHE   0.012   0.002   PHE C   4 
 TRP   0.014   0.002   TRP A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3756)
  covalent geometry    : angle       0.57963 ( 5117)
  hydrogen bonds       : bond        0.03334 (  150)
  hydrogen bonds       : angle       4.38250 (  492)

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

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

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.8813 (pp30) cc_final: 0.8374 (pp30)
REVERT: A   40 GLN cc_start: 0.8655 (tp40) cc_final: 0.8414 (tp-100)
REVERT: B   27 ASN cc_start: 0.7869 (m-40) cc_final: 0.7435 (t0)
REVERT: D   82 TRP cc_start: 0.8624 (p-90) cc_final: 0.8265 (p90)
REVERT: D  125 ASN cc_start: 0.7532 (OUTLIER) cc_final: 0.7103 (m110)
  outliers start: 9
  outliers final: 7
  residues processed: 61
  average time/residue: 0.0468
  time to fit residues: 3.9501
Evaluate side-chains
  61 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  125 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 43 optimal weight:   20.0000
   chunk 17 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9980
   chunk 25 optimal weight:    9.9990
   chunk 19 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
B  40 GLN
C  87 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.152473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.120847 restraints weight = 4575.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.123252 restraints weight = 3418.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.124808 restraints weight = 2835.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.125639 restraints weight = 2514.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.126489 restraints weight = 2334.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3756  Z= 0.144
  Angle     :  0.597   7.899   5117  Z= 0.304
  Chirality :  0.045   0.129    610
  Planarity :  0.005   0.078    659
  Dihedral  :  5.782  79.641    518
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 18.97 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.55 (0.39), residues: 478
  helix:  1.30 (0.50), residues: 101
  sheet: -1.29 (0.41), residues: 176
  loop : -1.95 (0.43), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  83 
 TYR   0.011   0.001   TYR D  85 
 PHE   0.011   0.002   PHE C   4 
 TRP   0.015   0.002   TRP A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 3756)
  covalent geometry    : angle       0.59699 ( 5117)
  hydrogen bonds       : bond        0.03525 (  150)
  hydrogen bonds       : angle       4.38674 (  492)

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

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

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.8870 (pp30) cc_final: 0.8458 (pp30)
REVERT: A   40 GLN cc_start: 0.8638 (tp40) cc_final: 0.8389 (tp-100)
REVERT: B   27 ASN cc_start: 0.7816 (m-40) cc_final: 0.7460 (t0)
  outliers start: 9
  outliers final: 8
  residues processed: 63
  average time/residue: 0.0448
  time to fit residues: 3.8956
Evaluate side-chains
  62 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   87 ASN
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain D residue   48 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 1 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 45 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 34 optimal weight:    7.9990
   chunk 0 optimal weight:    0.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
C  87 ASN
D 125 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.150237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.118692 restraints weight = 4577.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.120911 restraints weight = 3502.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.122558 restraints weight = 2930.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.123503 restraints weight = 2597.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.124266 restraints weight = 2399.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3756  Z= 0.209
  Angle     :  0.655   8.253   5117  Z= 0.332
  Chirality :  0.046   0.143    610
  Planarity :  0.006   0.082    659
  Dihedral  :  6.103  85.356    518
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 20.44 %
    Favored  : 76.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (0.39), residues: 478
  helix:  1.21 (0.51), residues: 101
  sheet: -1.38 (0.43), residues: 164
  loop : -2.08 (0.41), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  83 
 TYR   0.010   0.002   TYR D  85 
 PHE   0.012   0.002   PHE D   4 
 TRP   0.018   0.002   TRP A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 ( 3756)
  covalent geometry    : angle       0.65545 ( 5117)
  hydrogen bonds       : bond        0.03937 (  150)
  hydrogen bonds       : angle       4.56675 (  492)

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

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

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.8903 (pp30) cc_final: 0.8503 (pp30)
REVERT: A   40 GLN cc_start: 0.8666 (tp40) cc_final: 0.8409 (tp-100)
REVERT: B   27 ASN cc_start: 0.7905 (m-40) cc_final: 0.7502 (t0)
  outliers start: 11
  outliers final: 9
  residues processed: 62
  average time/residue: 0.0436
  time to fit residues: 3.7954
Evaluate side-chains
  64 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   87 ASN
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain D residue   48 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   chunk 14 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 26 optimal weight:    0.2980
   chunk 19 optimal weight:    8.9990
   overall best weight:    2.0588

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

Flipped N/Q/H residues before XYZ refinement:
B  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.152089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.120353 restraints weight = 4530.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.122723 restraints weight = 3444.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.124414 restraints weight = 2855.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.125391 restraints weight = 2528.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.126220 restraints weight = 2334.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3756  Z= 0.154
  Angle     :  0.636   8.115   5117  Z= 0.318
  Chirality :  0.046   0.131    610
  Planarity :  0.006   0.082    659
  Dihedral  :  6.111  88.404    518
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 21.43 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.63 (0.39), residues: 478
  helix:  1.30 (0.50), residues: 101
  sheet: -1.35 (0.41), residues: 176
  loop : -2.02 (0.42), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  83 
 TYR   0.008   0.001   TYR D  42 
 PHE   0.025   0.002   PHE D  95 
 TRP   0.016   0.002   TRP A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 3756)
  covalent geometry    : angle       0.63612 ( 5117)
  hydrogen bonds       : bond        0.03671 (  150)
  hydrogen bonds       : angle       4.45501 (  492)

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

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

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.8884 (pp30) cc_final: 0.8474 (pp30)
REVERT: A   40 GLN cc_start: 0.8670 (tp40) cc_final: 0.8461 (tp-100)
REVERT: B   27 ASN cc_start: 0.7941 (m-40) cc_final: 0.7517 (t0)
  outliers start: 9
  outliers final: 7
  residues processed: 61
  average time/residue: 0.0458
  time to fit residues: 3.8910
Evaluate side-chains
  60 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain D residue   48 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0570
   chunk 39 optimal weight:    7.9990
   chunk 8 optimal weight:    7.9990
   chunk 0 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.5302

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

Flipped N/Q/H residues before XYZ refinement:
B  40 GLN
C  87 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.154005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.122484 restraints weight = 4532.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.124899 restraints weight = 3384.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.126429 restraints weight = 2807.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.127688 restraints weight = 2486.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.128283 restraints weight = 2280.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3756  Z= 0.131
  Angle     :  0.609   8.179   5117  Z= 0.305
  Chirality :  0.045   0.136    610
  Planarity :  0.006   0.082    659
  Dihedral  :  5.991  88.197    518
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 21.92 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.39), residues: 478
  helix:  1.42 (0.50), residues: 101
  sheet: -1.31 (0.41), residues: 182
  loop : -1.90 (0.43), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  83 
 TYR   0.007   0.001   TYR D  42 
 PHE   0.024   0.002   PHE D  95 
 TRP   0.017   0.002   TRP A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3756)
  covalent geometry    : angle       0.60855 ( 5117)
  hydrogen bonds       : bond        0.03441 (  150)
  hydrogen bonds       : angle       4.38105 (  492)

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

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

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A    6 GLN cc_start: 0.8871 (pp30) cc_final: 0.8466 (pp30)
REVERT: A   40 GLN cc_start: 0.8661 (tp40) cc_final: 0.8457 (tp-100)
REVERT: B   27 ASN cc_start: 0.7921 (m-40) cc_final: 0.7492 (t0)
  outliers start: 7
  outliers final: 7
  residues processed: 62
  average time/residue: 0.0419
  time to fit residues: 3.6781
Evaluate side-chains
  61 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  105 VAL
Chi-restraints excluded: chain C residue   87 ASN
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain D residue   48 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 14 optimal weight:    0.4980
   chunk 22 optimal weight:    0.5980
   chunk 18 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 47 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 4 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C  87 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.154176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.122652 restraints weight = 4461.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.125059 restraints weight = 3342.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.126853 restraints weight = 2768.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.127864 restraints weight = 2441.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.128760 restraints weight = 2249.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086   3756  Z= 0.220
  Angle     :  1.245  59.198   5117  Z= 0.721
  Chirality :  0.070   1.330    610
  Planarity :  0.006   0.081    659
  Dihedral  :  6.309  88.135    518
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 22.41 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.49 (0.39), residues: 478
  helix:  1.46 (0.50), residues: 101
  sheet: -1.34 (0.41), residues: 182
  loop : -1.89 (0.43), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  83 
 TYR   0.006   0.001   TYR D  42 
 PHE   0.023   0.002   PHE D  95 
 TRP   0.016   0.002   TRP A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 3756)
  covalent geometry    : angle       1.24476 ( 5117)
  hydrogen bonds       : bond        0.04611 (  150)
  hydrogen bonds       : angle       4.37370 (  492)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 729.90 seconds
wall clock time: 13 minutes 22.20 seconds (802.20 seconds total)