Starting phenix.real_space_refine
on Tue Feb  3 16:25:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9pv4_71882/02_2026/9pv4_71882.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9pv4_71882/02_2026/9pv4_71882.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9pv4_71882/02_2026/9pv4_71882.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9pv4_71882/02_2026/9pv4_71882.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9pv4_71882/02_2026/9pv4_71882.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9pv4_71882/02_2026/9pv4_71882.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
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      18      5.16       5
     C    3067      2.51       5
     N     816      2.21       5
     O     930      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4831
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 928
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 4, 'TRANS': 114}
    Chain: "B"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 821
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101}
    Chain: "C"
      Number of atoms: 1229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1229
          Classifications: {'peptide': 152}
          Link IDs: {'PTRANS': 8, 'TRANS': 143}
    Chain: "H"
      Number of atoms: 1025
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1025
          Classifications: {'peptide': 130}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 122}
    Chain: "L"
      Number of atoms: 814
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 814
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 4, 'TRANS': 103}
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 0.89, per 1000 atoms: 0.18
  Number of scatterers: 4831
  At special positions: 0
  Unit cell: (55.825, 68.875, 121.075, 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      18     16.00
     O     930      8.00
     N     816      7.00
     C    3067      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.02

  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
  Links applied
    NAG-ASN
      " NAG C 201 " - " ASN C  74 "
  Time building additional restraints: 0.36
  Conformation dependent library (CDL) restraints added in 296.3 milliseconds
  

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1108

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 11 sheets defined
      16.2% alpha, 38.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 67
      No H-bonds generated for 'chain 'A' and resid 65 through 67'
    Processing helix  chain 'A' and resid 88 through 92
    Processing helix  chain 'B' and resid 79 through 83
    Processing helix  chain 'C' and resid 14 through 20
    Processing helix  chain 'C' and resid 26 through 38
    Processing helix  chain 'C' and resid 97 through 113
    Processing helix  chain 'C' and resid 114 through 122
    Processing helix  chain 'C' and resid 125 through 140
    Processing helix  chain 'C' and resid 149 through 151
      No H-bonds generated for 'chain 'C' and resid 149 through 151'
    Processing helix  chain 'H' and resid 64 through 67
    Processing helix  chain 'H' and resid 76 through 78
      No H-bonds generated for 'chain 'H' and resid 76 through 78'
    Processing helix  chain 'H' and resid 89 through 93
    Processing helix  chain 'L' and resid 24 through 28
    Processing helix  chain 'L' and resid 77 through 81
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7
    Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12
      removed outlier: 6.901A  pdb=" N   VAL A  36 " --> pdb=" O   HIS A  52 " (cutoff:3.500A)
      removed outlier: 4.792A  pdb=" N   HIS A  52 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   TRP A  38 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.636A  pdb=" N   LEU B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   TYR B  49 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 48 through 50
      removed outlier: 6.435A  pdb=" N   GLY C  48 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
      removed outlier: 7.941A  pdb=" N   PHE C  91 " --> pdb=" O   GLY C  48 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ALA C  50 " --> pdb=" O   PHE C  91 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   LEU C  93 " --> pdb=" O   ALA C  50 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   ASP C  83 " --> pdb=" O   GLU C  77 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   GLU C  77 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   VAL C  89 " --> pdb=" O   LYS C  71 " (cutoff:3.500A)
      removed outlier: 11.073A  pdb=" N   LYS C  71 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
      removed outlier: 11.850A  pdb=" N   PHE C  91 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 12.304A  pdb=" N   LEU C  69 " --> pdb=" O   PHE C  91 " (cutoff:3.500A)
      removed outlier: 10.890A  pdb=" N   LEU C  93 " --> pdb=" O   GLY C  67 " (cutoff:3.500A)
      removed outlier: 12.117A  pdb=" N   GLY C  67 " --> pdb=" O   LEU C  93 " (cutoff:3.500A)
      removed outlier: 8.192A  pdb=" N   ARG C 154 " --> pdb=" O   ILE C  64 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   VAL C  66 " --> pdb=" O   ARG C 154 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   LEU C 156 " --> pdb=" O   VAL C  66 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   ILE C  68 " --> pdb=" O   LEU C 156 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.398A  pdb=" N   TRP H  33 " --> pdb=" O   THR H 101 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   MET H  34 " --> pdb=" O   ARG H  50 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   ARG H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.789A  pdb=" N   GLY H 102 " --> pdb=" O   PHE H 118 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   PHE H 118 " --> pdb=" O   GLY H 102 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   TYR H 104 " --> pdb=" O   GLU H 116 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   GLU H 116 " --> pdb=" O   TYR H 104 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 5
    Processing sheet with id=AB1, first strand: chain 'L' and resid 8 through 11
      removed outlier: 6.516A  pdb=" N   TRP L  33 " --> pdb=" O   LEU L  45 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 11

    202 hydrogen bonds defined for protein.
    483 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: 0.63

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 866
        1.31 -     1.44: 1381
        1.44 -     1.56: 2632
        1.56 -     1.69: 43
        1.69 -     1.81: 28
  Bond restraints: 4950
  Sorted by residual:
  bond pdb=" CB  HIS B  90 "
       pdb=" CG  HIS B  90 "
    ideal  model  delta    sigma   weight residual
    1.497  1.409  0.088 1.40e-02 5.10e+03 4.00e+01
  bond pdb=" CB  LEU L 108 "
       pdb=" CG  LEU L 108 "
    ideal  model  delta    sigma   weight residual
    1.530  1.656 -0.126 2.00e-02 2.50e+03 3.97e+01
  bond pdb=" CG  TYR L   1 "
       pdb=" CD2 TYR L   1 "
    ideal  model  delta    sigma   weight residual
    1.389  1.490 -0.101 2.10e-02 2.27e+03 2.32e+01
  bond pdb=" CG  TYR B  96 "
       pdb=" CD1 TYR B  96 "
    ideal  model  delta    sigma   weight residual
    1.389  1.290  0.099 2.10e-02 2.27e+03 2.21e+01
  bond pdb=" CG  TYR L   1 "
       pdb=" CD1 TYR L   1 "
    ideal  model  delta    sigma   weight residual
    1.389  1.487 -0.098 2.10e-02 2.27e+03 2.19e+01
  ... (remaining 4945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.55: 5885
        2.55 -     5.10: 714
        5.10 -     7.66: 106
        7.66 -    10.21: 7
       10.21 -    12.76: 2
  Bond angle restraints: 6714
  Sorted by residual:
  angle pdb=" C   GLU C  77 "
        pdb=" N   TRP C  78 "
        pdb=" CA  TRP C  78 "
      ideal   model   delta    sigma   weight residual
     120.63  133.39  -12.76 1.61e+00 3.86e-01 6.28e+01
  angle pdb=" N   GLY A 112 "
        pdb=" CA  GLY A 112 "
        pdb=" C   GLY A 112 "
      ideal   model   delta    sigma   weight residual
     111.64  123.47  -11.83 1.57e+00 4.06e-01 5.68e+01
  angle pdb=" C   GLY H  53 "
        pdb=" N   PRO H  54 "
        pdb=" CA  PRO H  54 "
      ideal   model   delta    sigma   weight residual
     119.56  126.92   -7.36 1.01e+00 9.80e-01 5.32e+01
  angle pdb=" C   GLY A   8 "
        pdb=" N   PRO A   9 "
        pdb=" CA  PRO A   9 "
      ideal   model   delta    sigma   weight residual
     120.03  126.54   -6.51 9.90e-01 1.02e+00 4.32e+01
  angle pdb=" C   GLN H  39 "
        pdb=" N   PRO H  40 "
        pdb=" CA  PRO H  40 "
      ideal   model   delta    sigma   weight residual
     119.66  124.33   -4.67 7.30e-01 1.88e+00 4.09e+01
  ... (remaining 6709 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.28: 2775
       15.28 -    30.55: 90
       30.55 -    45.82: 23
       45.82 -    61.10: 16
       61.10 -    76.37: 4
  Dihedral angle restraints: 2908
    sinusoidal: 1159
      harmonic: 1749
  Sorted by residual:
  dihedral pdb=" N   PHE C  75 "
           pdb=" C   PHE C  75 "
           pdb=" CA  PHE C  75 "
           pdb=" CB  PHE C  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.73   -7.93     0      2.50e+00 1.60e-01 1.01e+01
  dihedral pdb=" CA  GLU A 102 "
           pdb=" CB  GLU A 102 "
           pdb=" CG  GLU A 102 "
           pdb=" CD  GLU A 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  124.07   55.93     3      1.50e+01 4.44e-03 9.37e+00
  dihedral pdb=" C   PHE C  75 "
           pdb=" N   PHE C  75 "
           pdb=" CA  PHE C  75 "
           pdb=" CB  PHE C  75 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.92    7.32     0      2.50e+00 1.60e-01 8.58e+00
  ... (remaining 2905 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 480
       0.090 -    0.179: 191
       0.179 -    0.269: 41
       0.269 -    0.358: 3
       0.358 -    0.448: 3
  Chirality restraints: 718
  Sorted by residual:
  chirality pdb=" C2  NAG C 201 "
            pdb=" C1  NAG C 201 "
            pdb=" C3  NAG C 201 "
            pdb=" N2  NAG C 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.94    0.45 2.00e-01 2.50e+01 5.01e+00
  chirality pdb=" CG  LEU L 108 "
            pdb=" CB  LEU L 108 "
            pdb=" CD1 LEU L 108 "
            pdb=" CD2 LEU L 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -3.01    0.42 2.00e-01 2.50e+01 4.42e+00
  chirality pdb=" C1  NAG C 201 "
            pdb=" ND2 ASN C  74 "
            pdb=" C2  NAG C 201 "
            pdb=" O5  NAG C 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.79    0.39 2.00e-01 2.50e+01 3.71e+00
  ... (remaining 715 not shown)

  Planarity restraints: 865
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  34 "   -0.065 2.00e-02 2.50e+03   3.62e-02 2.62e+01
        pdb=" CG  TYR L  34 "    0.017 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  34 "    0.029 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  34 "    0.028 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  34 "    0.018 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  34 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  34 "    0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR L  34 "   -0.058 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 152 "   -0.053 2.00e-02 2.50e+03   2.98e-02 1.78e+01
        pdb=" CG  TYR C 152 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 152 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 152 "    0.017 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 152 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 152 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 152 "    0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR C 152 "   -0.049 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  96 "   -0.047 2.00e-02 2.50e+03   2.46e-02 1.21e+01
        pdb=" CG  TYR A  96 "    0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  96 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  96 "    0.016 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  96 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  96 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  96 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A  96 "   -0.034 2.00e-02 2.50e+03
  ... (remaining 862 not shown)

  Histogram of nonbonded interaction distances:
        1.32 -     2.04: 2
        2.04 -     2.75: 811
        2.75 -     3.47: 6304
        3.47 -     4.18: 12416
        4.18 -     4.90: 20501
  Nonbonded interactions: 40034
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 102 "
            pdb=" OD1 ASP A 103 "
     model   vdw
     1.323 3.040
  nonbonded pdb=" OE1 GLU C 128 "
            pdb=" NH2 ARG C 131 "
     model   vdw
     1.552 3.120
  nonbonded pdb=" C   GLU A 102 "
            pdb=" OD1 ASP A 103 "
     model   vdw
     2.231 3.270
  nonbonded pdb=" O   ASN B  50 "
            pdb=" OD1 ASN B  50 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OD1 ASP A 107 "
            pdb=" N   VAL A 108 "
     model   vdw
     2.293 3.120
  ... (remaining 40029 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             5.520
  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:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.200
  Find NCS groups from input model:        0.020
  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:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6919
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      :  0.018   0.126   4953  Z= 0.958
  Angle     :  1.751  12.761   6721  Z= 1.183
  Chirality :  0.096   0.448    718
  Planarity :  0.009   0.046    864
  Dihedral  : 10.259  76.373   1794
  Min Nonbonded Distance : 1.323

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.32), residues: 606
  helix: -0.48 (0.51), residues: 67
  sheet:  1.19 (0.34), residues: 206
  loop :  0.96 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  99 
 TYR   0.065   0.009   TYR L  34 
 PHE   0.047   0.007   PHE C  75 
 TRP   0.038   0.009   TRP H 108 
 HIS   0.008   0.003   HIS C 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.01843 ( 4950)
  covalent geometry    : angle       1.74981 ( 6714)
  SS BOND              : bond        0.00522 (    2)
  SS BOND              : angle       2.62129 (    4)
  hydrogen bonds       : bond        0.15034 (  190)
  hydrogen bonds       : angle       8.68602 (  483)
  link_NAG-ASN         : bond        0.08110 (    1)
  link_NAG-ASN         : angle       2.72546 (    3)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 LEU cc_start: 0.8011 (mt) cc_final: 0.7776 (mp)
REVERT: A   19 SER cc_start: 0.8423 (t) cc_final: 0.8179 (p)
REVERT: A   24 PHE cc_start: 0.7655 (t80) cc_final: 0.7147 (t80)
REVERT: A   62 ASN cc_start: 0.9047 (t0) cc_final: 0.8823 (t0)
REVERT: A   73 LYS cc_start: 0.7822 (ttpt) cc_final: 0.7306 (ttmt)
REVERT: B   22 THR cc_start: 0.9185 (m) cc_final: 0.8772 (t)
REVERT: B   38 GLN cc_start: 0.7950 (tt0) cc_final: 0.7628 (tt0)
REVERT: B   54 LEU cc_start: 0.7702 (mt) cc_final: 0.7457 (mt)
REVERT: B   77 SER cc_start: 0.8903 (m) cc_final: 0.8593 (m)
REVERT: B   92 TRP cc_start: 0.7911 (t-100) cc_final: 0.7662 (t60)
REVERT: H   17 SER cc_start: 0.7747 (p) cc_final: 0.7367 (m)
REVERT: H   21 SER cc_start: 0.8222 (m) cc_final: 0.7774 (p)
REVERT: H   46 GLU cc_start: 0.6874 (tt0) cc_final: 0.6594 (tt0)
REVERT: H  111 TYR cc_start: 0.8583 (t80) cc_final: 0.8191 (t80)
REVERT: H  116 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7052 (mt-10)
REVERT: L   11 VAL cc_start: 0.7391 (t) cc_final: 0.7150 (t)
REVERT: L   22 ARG cc_start: 0.8010 (mtm180) cc_final: 0.7525 (ttm-80)
REVERT: L   24 ASP cc_start: 0.8235 (m-30) cc_final: 0.7969 (m-30)
REVERT: L   85 TYR cc_start: 0.9159 (m-80) cc_final: 0.8911 (m-10)
REVERT: L   90 ASP cc_start: 0.8455 (p0) cc_final: 0.8203 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 253
  average time/residue: 0.0853
  time to fit residues: 26.0350
Evaluate side-chains
  147 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 56 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
A  86 ASN
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  50 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.157582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.141668 restraints weight = 9339.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.145808 restraints weight = 5296.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.148582 restraints weight = 3414.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.150484 restraints weight = 2400.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.151826 restraints weight = 1781.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.4062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   4953  Z= 0.201
  Angle     :  0.799   8.167   6721  Z= 0.432
  Chirality :  0.052   0.226    718
  Planarity :  0.006   0.045    864
  Dihedral  :  5.332  24.889    693
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 15.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 13.85 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.34), residues: 606
  helix:  1.24 (0.63), residues: 61
  sheet:  0.94 (0.32), residues: 233
  loop :  0.48 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H 100 
 TYR   0.023   0.002   TYR L  47 
 PHE   0.028   0.004   PHE C  75 
 TRP   0.027   0.002   TRP C  78 
 HIS   0.004   0.001   HIS B  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 4950)
  covalent geometry    : angle       0.79701 ( 6714)
  SS BOND              : bond        0.00182 (    2)
  SS BOND              : angle       0.74652 (    4)
  hydrogen bonds       : bond        0.05526 (  190)
  hydrogen bonds       : angle       6.62804 (  483)
  link_NAG-ASN         : bond        0.01034 (    1)
  link_NAG-ASN         : angle       2.94952 (    3)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 168
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.6569 (pm20) cc_final: 0.6051 (tt0)
REVERT: B   54 LEU cc_start: 0.7898 (mt) cc_final: 0.7670 (mt)
REVERT: B   92 TRP cc_start: 0.8180 (t-100) cc_final: 0.7818 (t60)
REVERT: C   11 ARG cc_start: 0.7920 (tpp80) cc_final: 0.7564 (tpp80)
REVERT: C   75 PHE cc_start: 0.5709 (OUTLIER) cc_final: 0.4506 (p90)
REVERT: C  138 SER cc_start: 0.8041 (m) cc_final: 0.7468 (t)
REVERT: H  111 TYR cc_start: 0.8421 (t80) cc_final: 0.8199 (t80)
REVERT: L   22 ARG cc_start: 0.8137 (mtm180) cc_final: 0.7855 (ttm-80)
REVERT: L   85 TYR cc_start: 0.8944 (m-80) cc_final: 0.8741 (m-10)
  outliers start: 30
  outliers final: 12
  residues processed: 184
  average time/residue: 0.0520
  time to fit residues: 12.1390
Evaluate side-chains
  153 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain C residue   62 ASN
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain H residue   50 ARG
Chi-restraints excluded: chain H residue   77 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 17 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
A  86 ASN
** B  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  43 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.147511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.131035 restraints weight = 9443.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.134984 restraints weight = 5526.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.137624 restraints weight = 3673.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.139505 restraints weight = 2662.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.140914 restraints weight = 2043.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.5222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   4953  Z= 0.262
  Angle     :  0.791   7.538   6721  Z= 0.420
  Chirality :  0.051   0.202    718
  Planarity :  0.006   0.055    864
  Dihedral  :  5.384  23.704    693
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 18.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 19.23 %
    Favored  : 75.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.35), residues: 606
  helix:  1.09 (0.61), residues: 62
  sheet:  0.80 (0.33), residues: 246
  loop :  0.17 (0.39), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 100 
 TYR   0.024   0.002   TYR B  49 
 PHE   0.021   0.003   PHE C  75 
 TRP   0.021   0.002   TRP C  78 
 HIS   0.003   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00603 ( 4950)
  covalent geometry    : angle       0.78907 ( 6714)
  SS BOND              : bond        0.00210 (    2)
  SS BOND              : angle       1.04055 (    4)
  hydrogen bonds       : bond        0.05163 (  190)
  hydrogen bonds       : angle       6.35781 (  483)
  link_NAG-ASN         : bond        0.01068 (    1)
  link_NAG-ASN         : angle       2.74759 (    3)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.7212 (pm20) cc_final: 0.6729 (pp20)
REVERT: B   38 GLN cc_start: 0.7824 (tt0) cc_final: 0.7482 (tt0)
REVERT: B   54 LEU cc_start: 0.8231 (mt) cc_final: 0.7988 (mt)
REVERT: B   92 TRP cc_start: 0.8391 (t-100) cc_final: 0.7754 (t60)
REVERT: C   75 PHE cc_start: 0.5902 (OUTLIER) cc_final: 0.4605 (p90)
REVERT: C  138 SER cc_start: 0.8096 (m) cc_final: 0.7566 (t)
REVERT: C  150 ARG cc_start: 0.7950 (mtp85) cc_final: 0.7108 (ptp-110)
REVERT: H   73 SER cc_start: 0.7475 (t) cc_final: 0.7237 (t)
REVERT: L   85 TYR cc_start: 0.9003 (m-80) cc_final: 0.8703 (m-10)
  outliers start: 27
  outliers final: 20
  residues processed: 163
  average time/residue: 0.0727
  time to fit residues: 14.9723
Evaluate side-chains
  150 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   90 HIS
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   50 ARG
Chi-restraints excluded: chain H residue   77 SER
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue  107 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0070
   chunk 3 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 34 optimal weight:    0.3980
   chunk 36 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.4804

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
B  37 GLN
** B  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 119 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.144707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.128362 restraints weight = 9307.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.132202 restraints weight = 5280.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.134847 restraints weight = 3463.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.136565 restraints weight = 2465.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.138128 restraints weight = 1899.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.5986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4953  Z= 0.235
  Angle     :  0.753   7.961   6721  Z= 0.397
  Chirality :  0.049   0.214    718
  Planarity :  0.006   0.068    864
  Dihedral  :  5.400  23.800    693
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 17.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 20.77 %
    Favored  : 73.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.35), residues: 606
  helix:  1.04 (0.60), residues: 62
  sheet:  0.56 (0.34), residues: 236
  loop : -0.08 (0.37), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  19 
 TYR   0.037   0.003   TYR B  49 
 PHE   0.026   0.003   PHE H 118 
 TRP   0.017   0.002   TRP H  36 
 HIS   0.004   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 ( 4950)
  covalent geometry    : angle       0.75157 ( 6714)
  SS BOND              : bond        0.00126 (    2)
  SS BOND              : angle       0.85108 (    4)
  hydrogen bonds       : bond        0.04847 (  190)
  hydrogen bonds       : angle       6.29683 (  483)
  link_NAG-ASN         : bond        0.00798 (    1)
  link_NAG-ASN         : angle       2.28289 (    3)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 137
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 TYR cc_start: 0.7904 (m-80) cc_final: 0.7676 (m-80)
REVERT: B   38 GLN cc_start: 0.7805 (tt0) cc_final: 0.7334 (tt0)
REVERT: B   92 TRP cc_start: 0.8399 (t-100) cc_final: 0.7502 (t60)
REVERT: C   75 PHE cc_start: 0.6136 (OUTLIER) cc_final: 0.4825 (p90)
REVERT: C  138 SER cc_start: 0.8024 (m) cc_final: 0.7438 (t)
REVERT: C  150 ARG cc_start: 0.7925 (mtp85) cc_final: 0.7518 (ptp-110)
REVERT: C  151 GLU cc_start: 0.7380 (tp30) cc_final: 0.7028 (tp30)
REVERT: L   30 TYR cc_start: 0.6306 (m-80) cc_final: 0.5864 (m-80)
REVERT: L   85 TYR cc_start: 0.8959 (m-80) cc_final: 0.8697 (m-10)
REVERT: L  105 LEU cc_start: 0.8329 (tp) cc_final: 0.8046 (tp)
  outliers start: 29
  outliers final: 22
  residues processed: 159
  average time/residue: 0.0649
  time to fit residues: 13.4340
Evaluate side-chains
  153 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain B residue    2 ILE
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   90 HIS
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain H residue   50 ARG
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue  107 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 10 optimal weight:    0.4980
   chunk 22 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
B  30 HIS
B  37 GLN
** B  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.146998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.130760 restraints weight = 9372.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.134621 restraints weight = 5274.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.137267 restraints weight = 3450.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.139091 restraints weight = 2456.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.140534 restraints weight = 1881.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.6245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4953  Z= 0.169
  Angle     :  0.708   8.735   6721  Z= 0.370
  Chirality :  0.047   0.208    718
  Planarity :  0.005   0.063    864
  Dihedral  :  5.172  24.706    693
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 21.92 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.35), residues: 606
  helix:  1.26 (0.61), residues: 62
  sheet:  0.54 (0.34), residues: 242
  loop : -0.10 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  50 
 TYR   0.040   0.002   TYR B  49 
 PHE   0.019   0.002   PHE H 118 
 TRP   0.018   0.002   TRP C  78 
 HIS   0.004   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 4950)
  covalent geometry    : angle       0.70724 ( 6714)
  SS BOND              : bond        0.00233 (    2)
  SS BOND              : angle       0.83434 (    4)
  hydrogen bonds       : bond        0.04440 (  190)
  hydrogen bonds       : angle       6.21665 (  483)
  link_NAG-ASN         : bond        0.00577 (    1)
  link_NAG-ASN         : angle       2.01415 (    3)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 TYR cc_start: 0.7870 (m-80) cc_final: 0.7642 (m-80)
REVERT: B   38 GLN cc_start: 0.7821 (tt0) cc_final: 0.7336 (tt0)
REVERT: C   75 PHE cc_start: 0.5997 (OUTLIER) cc_final: 0.4771 (p90)
REVERT: C  109 LYS cc_start: 0.7676 (tttm) cc_final: 0.7285 (tttt)
REVERT: C  138 SER cc_start: 0.7934 (m) cc_final: 0.7397 (t)
REVERT: C  151 GLU cc_start: 0.7359 (tp30) cc_final: 0.7024 (tp30)
REVERT: H   20 LEU cc_start: 0.7968 (tp) cc_final: 0.7730 (tt)
REVERT: L   30 TYR cc_start: 0.6256 (m-80) cc_final: 0.6033 (m-80)
REVERT: L   85 TYR cc_start: 0.8973 (m-80) cc_final: 0.8714 (m-10)
REVERT: L  105 LEU cc_start: 0.8363 (tp) cc_final: 0.8089 (tp)
  outliers start: 25
  outliers final: 20
  residues processed: 160
  average time/residue: 0.0677
  time to fit residues: 14.0800
Evaluate side-chains
  152 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  111 LYS
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   90 HIS
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain H residue   50 ARG
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain H residue  125 THR
Chi-restraints excluded: chain L residue  107 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 49 optimal weight:    0.2980
   chunk 51 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 12 optimal weight:    7.9990
   chunk 28 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0270
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
B  37 GLN
** B  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 155 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.139245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.124996 restraints weight = 9361.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.128277 restraints weight = 5595.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.130611 restraints weight = 3746.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.132257 restraints weight = 2696.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.133440 restraints weight = 2052.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.6572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4953  Z= 0.147
  Angle     :  0.679   8.248   6721  Z= 0.355
  Chirality :  0.047   0.209    718
  Planarity :  0.005   0.057    864
  Dihedral  :  5.050  23.431    693
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 15.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 20.00 %
    Favored  : 74.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.35), residues: 606
  helix:  1.19 (0.62), residues: 62
  sheet:  0.48 (0.33), residues: 244
  loop : -0.17 (0.39), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  50 
 TYR   0.042   0.002   TYR B  49 
 PHE   0.019   0.002   PHE A  81 
 TRP   0.025   0.002   TRP B  92 
 HIS   0.004   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4950)
  covalent geometry    : angle       0.67845 ( 6714)
  SS BOND              : bond        0.00045 (    2)
  SS BOND              : angle       0.26867 (    4)
  hydrogen bonds       : bond        0.04176 (  190)
  hydrogen bonds       : angle       6.09360 (  483)
  link_NAG-ASN         : bond        0.00469 (    1)
  link_NAG-ASN         : angle       1.73058 (    3)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 137
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 TYR cc_start: 0.7775 (m-80) cc_final: 0.7501 (m-80)
REVERT: B    3 GLN cc_start: 0.6395 (mm110) cc_final: 0.6104 (mt0)
REVERT: B   38 GLN cc_start: 0.7742 (tt0) cc_final: 0.7419 (tt0)
REVERT: B   92 TRP cc_start: 0.8327 (t-100) cc_final: 0.7316 (t60)
REVERT: C   75 PHE cc_start: 0.5912 (OUTLIER) cc_final: 0.4686 (p90)
REVERT: C  109 LYS cc_start: 0.7746 (tttm) cc_final: 0.7336 (tttt)
REVERT: C  138 SER cc_start: 0.7843 (m) cc_final: 0.7330 (t)
REVERT: C  151 GLU cc_start: 0.7338 (tp30) cc_final: 0.7113 (tp30)
REVERT: H   20 LEU cc_start: 0.7912 (tp) cc_final: 0.7699 (tt)
REVERT: L   85 TYR cc_start: 0.8917 (m-80) cc_final: 0.8627 (m-80)
  outliers start: 31
  outliers final: 22
  residues processed: 159
  average time/residue: 0.0685
  time to fit residues: 13.9273
Evaluate side-chains
  155 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  111 LYS
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   90 HIS
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   50 ARG
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain H residue  125 THR
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue  107 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 22 optimal weight:    0.0980
   chunk 47 optimal weight:    0.1980
   chunk 15 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   chunk 8 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 33 optimal weight:    0.5980
   chunk 50 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0770
   overall best weight:    0.3538

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
B  37 GLN
C  34 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.140071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.125823 restraints weight = 9183.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.129058 restraints weight = 5581.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.131332 restraints weight = 3757.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.132972 restraints weight = 2722.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.134065 restraints weight = 2076.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.6674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4953  Z= 0.130
  Angle     :  0.680   7.401   6721  Z= 0.353
  Chirality :  0.047   0.206    718
  Planarity :  0.005   0.054    864
  Dihedral  :  4.917  24.744    693
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 21.73 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.35), residues: 606
  helix:  1.25 (0.64), residues: 62
  sheet:  0.42 (0.33), residues: 244
  loop : -0.23 (0.39), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  50 
 TYR   0.041   0.002   TYR B  49 
 PHE   0.018   0.002   PHE H 118 
 TRP   0.022   0.002   TRP H  47 
 HIS   0.005   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 4950)
  covalent geometry    : angle       0.67917 ( 6714)
  SS BOND              : bond        0.00216 (    2)
  SS BOND              : angle       0.53670 (    4)
  hydrogen bonds       : bond        0.04022 (  190)
  hydrogen bonds       : angle       5.91127 (  483)
  link_NAG-ASN         : bond        0.00388 (    1)
  link_NAG-ASN         : angle       1.55001 (    3)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6893 (mt)
REVERT: A  102 GLU cc_start: 0.7066 (pm20) cc_final: 0.6494 (pp20)
REVERT: B    3 GLN cc_start: 0.6562 (mm110) cc_final: 0.6353 (mp10)
REVERT: B   38 GLN cc_start: 0.7775 (tt0) cc_final: 0.7332 (tt0)
REVERT: C   75 PHE cc_start: 0.5683 (OUTLIER) cc_final: 0.4500 (p90)
REVERT: C  109 LYS cc_start: 0.7765 (tttm) cc_final: 0.7347 (tttt)
REVERT: C  138 SER cc_start: 0.7750 (m) cc_final: 0.7230 (t)
REVERT: H   20 LEU cc_start: 0.7866 (tp) cc_final: 0.7657 (tt)
REVERT: H   47 TRP cc_start: 0.8107 (OUTLIER) cc_final: 0.7380 (t-100)
REVERT: L   85 TYR cc_start: 0.8860 (m-80) cc_final: 0.8559 (m-80)
  outliers start: 26
  outliers final: 16
  residues processed: 158
  average time/residue: 0.0646
  time to fit residues: 13.1217
Evaluate side-chains
  151 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   90 HIS
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   50 ARG
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain H residue  125 THR
Chi-restraints excluded: chain L residue   97 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0970
   chunk 49 optimal weight:    0.3980
   chunk 39 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
B  37 GLN
** B  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.139723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.125418 restraints weight = 9375.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.128700 restraints weight = 5583.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.131022 restraints weight = 3743.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.132685 restraints weight = 2706.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.133773 restraints weight = 2060.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.6875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4953  Z= 0.139
  Angle     :  0.677   7.052   6721  Z= 0.350
  Chirality :  0.046   0.204    718
  Planarity :  0.005   0.051    864
  Dihedral  :  4.888  23.734    693
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 20.58 %
    Favored  : 73.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.36), residues: 606
  helix:  1.29 (0.64), residues: 62
  sheet:  0.42 (0.34), residues: 234
  loop : -0.21 (0.38), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H  19 
 TYR   0.038   0.002   TYR B  49 
 PHE   0.018   0.002   PHE H 118 
 TRP   0.030   0.002   TRP B  92 
 HIS   0.005   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4950)
  covalent geometry    : angle       0.67698 ( 6714)
  SS BOND              : bond        0.00109 (    2)
  SS BOND              : angle       0.56990 (    4)
  hydrogen bonds       : bond        0.03906 (  190)
  hydrogen bonds       : angle       5.84270 (  483)
  link_NAG-ASN         : bond        0.00434 (    1)
  link_NAG-ASN         : angle       1.20455 (    3)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 135
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6923 (mt)
REVERT: A  102 GLU cc_start: 0.7034 (pm20) cc_final: 0.6525 (pp20)
REVERT: B   38 GLN cc_start: 0.7754 (tt0) cc_final: 0.7337 (tt0)
REVERT: C   75 PHE cc_start: 0.5614 (OUTLIER) cc_final: 0.4451 (p90)
REVERT: C  109 LYS cc_start: 0.7763 (tttm) cc_final: 0.7341 (tttt)
REVERT: C  143 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8046 (mt)
REVERT: H   47 TRP cc_start: 0.8165 (OUTLIER) cc_final: 0.7613 (t-100)
REVERT: L   85 TYR cc_start: 0.8836 (m-80) cc_final: 0.8531 (m-80)
  outliers start: 30
  outliers final: 23
  residues processed: 158
  average time/residue: 0.0634
  time to fit residues: 12.8206
Evaluate side-chains
  156 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue   78 ASN
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   90 HIS
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  143 LEU
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   50 ARG
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain H residue  125 THR
Chi-restraints excluded: chain L residue    4 THR
Chi-restraints excluded: chain L residue   97 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 38 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0470
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
** B  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.138558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.125176 restraints weight = 9333.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.128173 restraints weight = 5686.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.130177 restraints weight = 3855.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.131797 restraints weight = 2861.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.132835 restraints weight = 2200.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.6987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4953  Z= 0.148
  Angle     :  0.705   8.027   6721  Z= 0.366
  Chirality :  0.047   0.208    718
  Planarity :  0.006   0.064    864
  Dihedral  :  4.989  23.411    693
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 21.15 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.35), residues: 606
  helix:  1.14 (0.61), residues: 62
  sheet:  0.40 (0.35), residues: 219
  loop : -0.28 (0.37), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C 150 
 TYR   0.022   0.002   TYR L  47 
 PHE   0.019   0.002   PHE A 105 
 TRP   0.032   0.002   TRP H  36 
 HIS   0.004   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 4950)
  covalent geometry    : angle       0.70501 ( 6714)
  SS BOND              : bond        0.00032 (    2)
  SS BOND              : angle       0.52464 (    4)
  hydrogen bonds       : bond        0.03941 (  190)
  hydrogen bonds       : angle       5.72574 (  483)
  link_NAG-ASN         : bond        0.00395 (    1)
  link_NAG-ASN         : angle       1.34609 (    3)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.7051 (pm20) cc_final: 0.6554 (pp20)
REVERT: B   38 GLN cc_start: 0.7810 (tt0) cc_final: 0.7285 (tt0)
REVERT: B   79 GLN cc_start: 0.6819 (OUTLIER) cc_final: 0.6457 (mp10)
REVERT: B   92 TRP cc_start: 0.8163 (t-100) cc_final: 0.7112 (t60)
REVERT: C   75 PHE cc_start: 0.5637 (OUTLIER) cc_final: 0.4543 (p90)
REVERT: C  109 LYS cc_start: 0.7768 (tttm) cc_final: 0.7346 (tttt)
REVERT: C  125 SER cc_start: 0.8127 (p) cc_final: 0.7266 (m)
REVERT: C  150 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.6782 (ptp-110)
REVERT: H   36 TRP cc_start: 0.7909 (m100) cc_final: 0.7497 (m100)
REVERT: H   47 TRP cc_start: 0.8242 (OUTLIER) cc_final: 0.7763 (t-100)
REVERT: L   85 TYR cc_start: 0.8849 (m-80) cc_final: 0.8550 (m-10)
  outliers start: 29
  outliers final: 22
  residues processed: 144
  average time/residue: 0.0677
  time to fit residues: 12.3960
Evaluate side-chains
  149 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 123
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain B residue    2 ILE
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain B residue   90 HIS
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  150 ARG
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   50 ARG
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain L residue    4 THR
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue  107 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 31 optimal weight:    0.1980
   chunk 3 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 142 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 = 0.3750 r_free = 0.3750 target = 0.137998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.124412 restraints weight = 9364.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.127408 restraints weight = 5790.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.129489 restraints weight = 3973.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.131060 restraints weight = 2950.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.132111 restraints weight = 2283.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.7189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4953  Z= 0.154
  Angle     :  0.704   8.403   6721  Z= 0.364
  Chirality :  0.047   0.213    718
  Planarity :  0.005   0.069    864
  Dihedral  :  4.928  22.954    693
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 21.92 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.35), residues: 606
  helix:  1.21 (0.61), residues: 62
  sheet:  0.37 (0.36), residues: 220
  loop : -0.32 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 150 
 TYR   0.023   0.002   TYR B  49 
 PHE   0.018   0.002   PHE H 118 
 TRP   0.025   0.002   TRP B  92 
 HIS   0.004   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 4950)
  covalent geometry    : angle       0.70335 ( 6714)
  SS BOND              : bond        0.00052 (    2)
  SS BOND              : angle       0.54518 (    4)
  hydrogen bonds       : bond        0.03906 (  190)
  hydrogen bonds       : angle       5.66201 (  483)
  link_NAG-ASN         : bond        0.00393 (    1)
  link_NAG-ASN         : angle       1.35728 (    3)

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

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

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1212 Ramachandran restraints generated.
    606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 126
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 GLU cc_start: 0.7040 (pm20) cc_final: 0.6691 (pp20)
REVERT: B   11 LEU cc_start: 0.9044 (tt) cc_final: 0.8737 (tt)
REVERT: B   38 GLN cc_start: 0.7838 (tt0) cc_final: 0.7476 (tt0)
REVERT: B   79 GLN cc_start: 0.6869 (mp10) cc_final: 0.6512 (mp10)
REVERT: C  109 LYS cc_start: 0.7768 (tttm) cc_final: 0.7320 (tttt)
REVERT: C  150 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.6569 (ptp-110)
REVERT: H   36 TRP cc_start: 0.7949 (m100) cc_final: 0.7499 (m100)
REVERT: H   47 TRP cc_start: 0.8268 (OUTLIER) cc_final: 0.7900 (t-100)
REVERT: L   79 GLU cc_start: 0.6620 (pm20) cc_final: 0.6369 (pm20)
  outliers start: 25
  outliers final: 22
  residues processed: 145
  average time/residue: 0.0735
  time to fit residues: 13.6015
Evaluate side-chains
  147 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain B residue    2 ILE
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   90 HIS
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  150 ARG
Chi-restraints excluded: chain H residue   47 TRP
Chi-restraints excluded: chain H residue   50 ARG
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain H residue  101 THR
Chi-restraints excluded: chain L residue    4 THR
Chi-restraints excluded: chain L residue   97 SER
Chi-restraints excluded: chain L residue  107 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 40 optimal weight:    0.3980
   chunk 45 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0170
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.5218

-------------------------------------------------------------------------------
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 = 0.3754 r_free = 0.3754 target = 0.138249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.125272 restraints weight = 9459.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.128211 restraints weight = 5707.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.130328 restraints weight = 3841.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.131518 restraints weight = 2789.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.132751 restraints weight = 2217.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.7317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4953  Z= 0.137
  Angle     :  0.700   8.678   6721  Z= 0.360
  Chirality :  0.047   0.215    718
  Planarity :  0.005   0.071    864
  Dihedral  :  4.962  22.561    693
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 22.31 %
    Favored  : 72.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.35), residues: 606
  helix:  1.25 (0.61), residues: 62
  sheet:  0.36 (0.35), residues: 220
  loop : -0.38 (0.37), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 150 
 TYR   0.024   0.002   TYR B  49 
 PHE   0.024   0.002   PHE A 105 
 TRP   0.022   0.002   TRP B  92 
 HIS   0.005   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4950)
  covalent geometry    : angle       0.69691 ( 6714)
  SS BOND              : bond        0.00448 (    2)
  SS BOND              : angle       2.77723 (    4)
  hydrogen bonds       : bond        0.03817 (  190)
  hydrogen bonds       : angle       5.39681 (  483)
  link_NAG-ASN         : bond        0.00349 (    1)
  link_NAG-ASN         : angle       1.36134 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 980.00 seconds
wall clock time: 17 minutes 41.93 seconds (1061.93 seconds total)