Starting phenix.real_space_refine
on Wed Mar  4 15:44:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pey_13361/03_2026/7pey_13361.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pey_13361/03_2026/7pey_13361.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pey_13361/03_2026/7pey_13361.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pey_13361/03_2026/7pey_13361.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pey_13361/03_2026/7pey_13361.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pey_13361/03_2026/7pey_13361.cif"
  }
  resolution = 4.5
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     342      5.49       5
     S      10      5.16       5
     C    7159      2.51       5
     N    2464      2.21       5
     O    3124      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13099
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "K"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "L"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "M"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "N"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "O"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "P"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "Q"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "R"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "J"
      Number of atoms: 3532
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 3532
          Classifications: {'DNA': 171}
          Link IDs: {'rna3p': 170}
    Chain: "I"
      Number of atoms: 3479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 3479
          Classifications: {'DNA': 171}
          Link IDs: {'rna3p': 170}
  Time building chain proxies: 2.90, per 1000 atoms: 0.22
  Number of scatterers: 13099
  At special positions: 0
  Unit cell: (150.15, 130.2, 116.55, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     342     15.00
     O    3124      8.00
     N    2464      7.00
     C    7159      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Conformation dependent library (CDL) restraints added in 419.6 milliseconds
  

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 8 sheets defined
      72.0% alpha, 2.1% beta
      166 base pairs and 301 stacking pairs defined.
    Time for finding SS restraints: 2.26
  Creating SS restraints...
    Processing helix  chain 'K' and resid 44 through 57
    Processing helix  chain 'K' and resid 63 through 79
      removed outlier: 3.700A  pdb=" N   PHE K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ASP K  77 " --> pdb=" O   GLU K  73 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   PHE K  78 " --> pdb=" O   ILE K  74 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 85 through 114
    Processing helix  chain 'K' and resid 120 through 132
      removed outlier: 3.819A  pdb=" N   ILE K 124 " --> pdb=" O   MET K 120 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 24 through 29
      removed outlier: 4.055A  pdb=" N   GLN L  27 " --> pdb=" O   ASP L  24 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ILE L  29 " --> pdb=" O   ILE L  26 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 30 through 41
    Processing helix  chain 'L' and resid 50 through 76
    Processing helix  chain 'L' and resid 82 through 93
    Processing helix  chain 'M' and resid 16 through 21
    Processing helix  chain 'M' and resid 26 through 36
    Processing helix  chain 'M' and resid 45 through 73
      removed outlier: 4.079A  pdb=" N   VAL M  49 " --> pdb=" O   ALA M  45 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 79 through 89
    Processing helix  chain 'M' and resid 90 through 97
    Processing helix  chain 'M' and resid 112 through 116
    Processing helix  chain 'N' and resid 37 through 49
      removed outlier: 3.869A  pdb=" N   VAL N  41 " --> pdb=" O   TYR N  37 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 55 through 84
    Processing helix  chain 'N' and resid 90 through 102
      removed outlier: 3.531A  pdb=" N   ILE N  94 " --> pdb=" O   THR N  90 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 103 through 123
    Processing helix  chain 'O' and resid 44 through 57
    Processing helix  chain 'O' and resid 63 through 77
    Processing helix  chain 'O' and resid 85 through 114
    Processing helix  chain 'O' and resid 120 through 131
      removed outlier: 3.580A  pdb=" N   ILE O 124 " --> pdb=" O   MET O 120 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 25 through 29
    Processing helix  chain 'P' and resid 30 through 41
    Processing helix  chain 'P' and resid 49 through 76
      removed outlier: 4.023A  pdb=" N   GLU P  53 " --> pdb=" O   LEU P  49 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP P  68 " --> pdb=" O   ASN P  64 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 82 through 93
      removed outlier: 3.503A  pdb=" N   VAL P  86 " --> pdb=" O   THR P  82 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   GLN P  93 " --> pdb=" O   ALA P  89 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 16 through 22
    Processing helix  chain 'Q' and resid 26 through 36
    Processing helix  chain 'Q' and resid 45 through 73
      removed outlier: 4.238A  pdb=" N   VAL Q  49 " --> pdb=" O   ALA Q  45 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 79 through 89
    Processing helix  chain 'Q' and resid 90 through 97
    Processing helix  chain 'Q' and resid 112 through 116
    Processing helix  chain 'R' and resid 37 through 49
    Processing helix  chain 'R' and resid 55 through 84
    Processing helix  chain 'R' and resid 90 through 102
    Processing helix  chain 'R' and resid 104 through 123
      removed outlier: 4.156A  pdb=" N   LYS R 108 " --> pdb=" O   GLY R 104 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84
      removed outlier: 6.447A  pdb=" N   ARG K  83 " --> pdb=" O   VAL L  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'K' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'L' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'M' and resid 42 through 43
      removed outlier: 7.475A  pdb=" N   ARG M  42 " --> pdb=" O   ILE N  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'M' and resid 101 through 102
      removed outlier: 7.080A  pdb=" N   THR M 101 " --> pdb=" O   TYR P  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'O' and resid 83 through 84
      removed outlier: 6.669A  pdb=" N   ARG O  83 " --> pdb=" O   VAL P  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'O' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'Q' and resid 42 through 43
      removed outlier: 7.151A  pdb=" N   ARG Q  42 " --> pdb=" O   ILE R  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    400 hydrogen bonds defined for protein.
    1179 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      429 hydrogen bonds
      858 hydrogen bond angles
      0 basepair planarities
      166 basepair parallelities
      301 stacking parallelities
  Total time for adding SS restraints: 3.07

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2792
        1.33 -     1.46: 4997
        1.46 -     1.58: 5541
        1.58 -     1.70: 682
        1.70 -     1.83: 20
  Bond restraints: 14032
  Sorted by residual:
  bond pdb=" N   GLU O  94 "
       pdb=" CA  GLU O  94 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.20e-02 6.94e+03 6.10e+00
  bond pdb=" N   LEU O  92 "
       pdb=" CA  LEU O  92 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.21e-02 6.83e+03 5.47e+00
  bond pdb=" N   GLN O  93 "
       pdb=" CA  GLN O  93 "
    ideal  model  delta    sigma   weight residual
    1.459  1.482 -0.022 1.18e-02 7.18e+03 3.63e+00
  bond pdb=" C3'  DG I 494 "
       pdb=" O3'  DG I 494 "
    ideal  model  delta    sigma   weight residual
    1.422  1.479 -0.057 3.00e-02 1.11e+03 3.59e+00
  bond pdb=" C3'  DG I 382 "
       pdb=" O3'  DG I 382 "
    ideal  model  delta    sigma   weight residual
    1.422  1.479 -0.057 3.00e-02 1.11e+03 3.56e+00
  ... (remaining 14027 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 19868
        2.31 -     4.61: 476
        4.61 -     6.92: 57
        6.92 -     9.23: 14
        9.23 -    11.54: 4
  Bond angle restraints: 20419
  Sorted by residual:
  angle pdb=" CB  LYS R  46 "
        pdb=" CG  LYS R  46 "
        pdb=" CD  LYS R  46 "
      ideal   model   delta    sigma   weight residual
     111.30  122.28  -10.98 2.30e+00 1.89e-01 2.28e+01
  angle pdb=" C   GLN O  93 "
        pdb=" CA  GLN O  93 "
        pdb=" CB  GLN O  93 "
      ideal   model   delta    sigma   weight residual
     110.95  118.24   -7.29 1.55e+00 4.16e-01 2.21e+01
  angle pdb=" N   GLU K  50 "
        pdb=" CA  GLU K  50 "
        pdb=" CB  GLU K  50 "
      ideal   model   delta    sigma   weight residual
     110.40  117.72   -7.32 1.63e+00 3.76e-01 2.02e+01
  angle pdb=" N   ILE M  79 "
        pdb=" CA  ILE M  79 "
        pdb=" C   ILE M  79 "
      ideal   model   delta    sigma   weight residual
     108.45  103.39    5.06 1.20e+00 6.94e-01 1.78e+01
  angle pdb=" N   LEU O  92 "
        pdb=" CA  LEU O  92 "
        pdb=" C   LEU O  92 "
      ideal   model   delta    sigma   weight residual
     111.28  106.73    4.55 1.09e+00 8.42e-01 1.74e+01
  ... (remaining 20414 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    36.00: 5768
       36.00 -    72.00: 1741
       72.00 -   107.99: 22
      107.99 -   143.99: 3
      143.99 -   179.99: 2
  Dihedral angle restraints: 7536
    sinusoidal: 5314
      harmonic: 2222
  Sorted by residual:
  dihedral pdb=" CA  ILE L  50 "
           pdb=" C   ILE L  50 "
           pdb=" N   TYR L  51 "
           pdb=" CA  TYR L  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.36  -23.64     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  PRO N 103 "
           pdb=" C   PRO N 103 "
           pdb=" N   GLY N 104 "
           pdb=" CA  GLY N 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.20   22.80     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  ASP N  51 "
           pdb=" C   ASP N  51 "
           pdb=" N   THR N  52 "
           pdb=" CA  THR N  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.05  -20.95     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 7533 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1730
       0.049 -    0.098: 486
       0.098 -    0.148: 90
       0.148 -    0.197: 8
       0.197 -    0.246: 6
  Chirality restraints: 2320
  Sorted by residual:
  chirality pdb=" CG  LEU M  23 "
            pdb=" CB  LEU M  23 "
            pdb=" CD1 LEU M  23 "
            pdb=" CD2 LEU M  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CA  LEU O  92 "
            pdb=" N   LEU O  92 "
            pdb=" C   LEU O  92 "
            pdb=" CB  LEU O  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CB  VAL O 101 "
            pdb=" CA  VAL O 101 "
            pdb=" CG1 VAL O 101 "
            pdb=" CG2 VAL O 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 2317 not shown)

  Planarity restraints: 1398
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS L  75 "   -0.035 2.00e-02 2.50e+03   2.80e-02 1.18e+01
        pdb=" CG  HIS L  75 "    0.052 2.00e-02 2.50e+03
        pdb=" ND1 HIS L  75 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 HIS L  75 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 HIS L  75 "   -0.024 2.00e-02 2.50e+03
        pdb=" NE2 HIS L  75 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR R  83 "   -0.027 2.00e-02 2.50e+03   2.18e-02 9.48e+00
        pdb=" CG  TYR R  83 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 TYR R  83 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR R  83 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR R  83 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR R  83 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR R  83 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR R  83 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE P 100 "   -0.014 2.00e-02 2.50e+03   2.22e-02 8.60e+00
        pdb=" CG  PHE P 100 "    0.050 2.00e-02 2.50e+03
        pdb=" CD1 PHE P 100 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 PHE P 100 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE1 PHE P 100 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE P 100 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE P 100 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1395 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 1084
        2.72 -     3.27: 11922
        3.27 -     3.81: 28286
        3.81 -     4.36: 32152
        4.36 -     4.90: 44433
  Nonbonded interactions: 117877
  Sorted by model distance:
  nonbonded pdb=" OH  TYR Q  39 "
            pdb=" OE1 GLU R  71 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" OG  SER M  40 "
            pdb=" O   ARG M  42 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   LEU O  61 "
            pdb=" NH2 ARG P  36 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" OD2 ASP K 106 "
            pdb=" NH2 ARG K 131 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" O   LEU M  85 "
            pdb=" ND2 ASN M  89 "
     model   vdw
     2.291 3.120
  ... (remaining 117872 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'K'
  selection = chain 'O'
}
ncs_group {
  reference = chain 'L'
  selection = chain 'P'
}
ncs_group {
  reference = chain 'M'
  selection = chain 'Q'
}
ncs_group {
  reference = chain 'N'
  selection = chain 'R'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.250
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
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      :  0.006   0.057  14032  Z= 0.275
  Angle     :  0.895  11.536  20419  Z= 0.510
  Chirality :  0.047   0.246   2320
  Planarity :  0.007   0.062   1398
  Dihedral  : 29.812 179.988   6104
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.28), residues: 752
  helix:  0.19 (0.21), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.36 (0.37), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG M  42 
 TYR   0.053   0.003   TYR R  83 
 PHE   0.050   0.003   PHE P 100 
 HIS   0.017   0.002   HIS L  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00596 (14032)
  covalent geometry    : angle       0.89517 (20419)
  hydrogen bonds       : bond        0.10384 (  829)
  hydrogen bonds       : angle       4.31032 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   50 GLU cc_start: 0.9460 (pm20) cc_final: 0.9031 (pm20)
REVERT: K   85 GLN cc_start: 0.9086 (mt0) cc_final: 0.8802 (mt0)
REVERT: K   90 MET cc_start: 0.9440 (mmp) cc_final: 0.9203 (mmp)
REVERT: K  120 MET cc_start: 0.8702 (mtm) cc_final: 0.8215 (mtt)
REVERT: L   75 HIS cc_start: 0.9443 (t70) cc_final: 0.8943 (t70)
REVERT: M   36 LYS cc_start: 0.9401 (mppt) cc_final: 0.9053 (mmtm)
REVERT: M   64 GLU cc_start: 0.9578 (mm-30) cc_final: 0.9301 (mm-30)
REVERT: M   79 ILE cc_start: 0.9590 (tp) cc_final: 0.9319 (pt)
REVERT: N   96 THR cc_start: 0.9683 (m) cc_final: 0.9463 (m)
REVERT: N   99 ARG cc_start: 0.9334 (mtp85) cc_final: 0.8543 (ttm110)
REVERT: N  102 LEU cc_start: 0.8854 (tp) cc_final: 0.8423 (tt)
REVERT: O   86 SER cc_start: 0.9826 (t) cc_final: 0.9545 (t)
REVERT: O   90 MET cc_start: 0.9660 (mmp) cc_final: 0.9186 (mmm)
REVERT: O  120 MET cc_start: 0.8299 (mtt) cc_final: 0.8035 (mtt)
REVERT: O  125 GLN cc_start: 0.9400 (mt0) cc_final: 0.9195 (mt0)
REVERT: P   72 TYR cc_start: 0.9560 (m-80) cc_final: 0.9259 (m-80)
REVERT: Q   87 ILE cc_start: 0.9480 (mm) cc_final: 0.9159 (mm)
REVERT: Q   90 ASP cc_start: 0.8905 (t70) cc_final: 0.8391 (t0)
REVERT: R   93 GLU cc_start: 0.9067 (mp0) cc_final: 0.8802 (mp0)
REVERT: R  113 GLU cc_start: 0.9357 (mm-30) cc_final: 0.9000 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1090
  time to fit residues: 27.5531
Evaluate side-chains
  116 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
K  93 GLN
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  38 ASN
M 104 GLN
O  55 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.034663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.027334 restraints weight = 182688.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.028214 restraints weight = 86404.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.028765 restraints weight = 51216.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.029203 restraints weight = 35163.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.029534 restraints weight = 26548.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14032  Z= 0.193
  Angle     :  0.612   7.419  20419  Z= 0.368
  Chirality :  0.034   0.133   2320
  Planarity :  0.005   0.057   1398
  Dihedral  : 32.331 179.086   4580
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  3.14 %
    Favored  : 96.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.30), residues: 752
  helix:  1.36 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop :  0.04 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG M  42 
 TYR   0.030   0.002   TYR R  83 
 PHE   0.026   0.002   PHE O 104 
 HIS   0.005   0.001   HIS L  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (14032)
  covalent geometry    : angle       0.61249 (20419)
  hydrogen bonds       : bond        0.04516 (  829)
  hydrogen bonds       : angle       3.18431 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 155
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9480 (m-10) cc_final: 0.8905 (m-80)
REVERT: K   59 GLU cc_start: 0.8956 (pm20) cc_final: 0.8737 (pm20)
REVERT: K   85 GLN cc_start: 0.9365 (mt0) cc_final: 0.9004 (mt0)
REVERT: K   90 MET cc_start: 0.9310 (mmp) cc_final: 0.8997 (mmp)
REVERT: K   94 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9234 (mm-30)
REVERT: K  120 MET cc_start: 0.8747 (mtm) cc_final: 0.8325 (mtt)
REVERT: K  123 ASP cc_start: 0.9709 (m-30) cc_final: 0.9504 (m-30)
REVERT: M   36 LYS cc_start: 0.9389 (mppt) cc_final: 0.8951 (mmtm)
REVERT: M   38 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.7812 (t0)
REVERT: M   56 GLU cc_start: 0.9361 (mt-10) cc_final: 0.9140 (mt-10)
REVERT: M  101 THR cc_start: 0.8856 (m) cc_final: 0.8569 (p)
REVERT: N   71 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8607 (mm-30)
REVERT: N  102 LEU cc_start: 0.8571 (tp) cc_final: 0.8283 (tp)
REVERT: O   67 PHE cc_start: 0.9092 (t80) cc_final: 0.8794 (t80)
REVERT: O   86 SER cc_start: 0.9778 (t) cc_final: 0.9464 (t)
REVERT: O   93 GLN cc_start: 0.9501 (pt0) cc_final: 0.9263 (pt0)
REVERT: O  104 PHE cc_start: 0.9191 (m-80) cc_final: 0.8663 (m-80)
REVERT: P   72 TYR cc_start: 0.9447 (m-80) cc_final: 0.9241 (m-80)
REVERT: R   76 GLU cc_start: 0.9353 (tp30) cc_final: 0.9089 (mt-10)
REVERT: R  101 LEU cc_start: 0.9456 (tt) cc_final: 0.9016 (tt)
REVERT: R  113 GLU cc_start: 0.9289 (mm-30) cc_final: 0.8972 (mm-30)
  outliers start: 4
  outliers final: 3
  residues processed: 157
  average time/residue: 0.0911
  time to fit residues: 21.7263
Evaluate side-chains
  114 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 110
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 76 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 1 optimal weight:    9.9990
   chunk 15 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   chunk 14 optimal weight:    7.9990
   chunk 6 optimal weight:    9.9990
   chunk 103 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
K  55 GLN
N 109 HIS
O  55 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.028266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2523 r_free = 0.2523 target = 0.020623 restraints weight = 179506.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.021386 restraints weight = 89231.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.021897 restraints weight = 55523.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2605 r_free = 0.2605 target = 0.022227 restraints weight = 39337.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.2617 r_free = 0.2617 target = 0.022498 restraints weight = 30618.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.3243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051  14032  Z= 0.310
  Angle     :  0.694   7.131  20419  Z= 0.410
  Chirality :  0.038   0.172   2320
  Planarity :  0.006   0.060   1398
  Dihedral  : 32.780 174.417   4580
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 18.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.93 %
    Favored  : 95.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.38 (0.29), residues: 752
  helix:  1.35 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.06 (0.38), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R  92 
 TYR   0.033   0.002   TYR R  83 
 PHE   0.026   0.003   PHE K 104 
 HIS   0.007   0.002   HIS P  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00668 (14032)
  covalent geometry    : angle       0.69432 (20419)
  hydrogen bonds       : bond        0.08099 (  829)
  hydrogen bonds       : angle       3.65332 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9547 (m-10) cc_final: 0.8989 (m-80)
REVERT: K   85 GLN cc_start: 0.9422 (mt0) cc_final: 0.8872 (mt0)
REVERT: K   90 MET cc_start: 0.9175 (mmp) cc_final: 0.8799 (mmp)
REVERT: K   94 GLU cc_start: 0.9391 (mm-30) cc_final: 0.9105 (mm-30)
REVERT: K  104 PHE cc_start: 0.9608 (m-80) cc_final: 0.9400 (m-10)
REVERT: K  120 MET cc_start: 0.8781 (mtm) cc_final: 0.8215 (mtt)
REVERT: M   41 GLU cc_start: 0.8409 (pm20) cc_final: 0.7915 (tm-30)
REVERT: M   56 GLU cc_start: 0.9367 (mt-10) cc_final: 0.9139 (mt-10)
REVERT: M   78 ILE cc_start: 0.9343 (pt) cc_final: 0.9140 (tp)
REVERT: M   90 ASP cc_start: 0.7228 (t0) cc_final: 0.6673 (t0)
REVERT: N   47 GLN cc_start: 0.9416 (mm-40) cc_final: 0.9140 (mm110)
REVERT: N   59 MET cc_start: 0.8581 (tpt) cc_final: 0.8336 (tpt)
REVERT: N   71 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8708 (mm-30)
REVERT: N  102 LEU cc_start: 0.8742 (tp) cc_final: 0.8418 (tp)
REVERT: N  105 GLU cc_start: 0.9614 (mp0) cc_final: 0.9349 (pm20)
REVERT: N  109 HIS cc_start: 0.9718 (m90) cc_final: 0.9349 (m170)
REVERT: O   76 GLN cc_start: 0.8992 (tp40) cc_final: 0.8623 (mm-40)
REVERT: O   86 SER cc_start: 0.9813 (t) cc_final: 0.9519 (p)
REVERT: O  100 LEU cc_start: 0.9755 (mt) cc_final: 0.9530 (mt)
REVERT: O  104 PHE cc_start: 0.9440 (m-80) cc_final: 0.8897 (m-80)
REVERT: O  120 MET cc_start: 0.8310 (mtt) cc_final: 0.7913 (mtt)
REVERT: P   72 TYR cc_start: 0.9552 (m-80) cc_final: 0.9148 (m-80)
REVERT: Q   36 LYS cc_start: 0.9427 (mppt) cc_final: 0.9174 (mmtm)
REVERT: R   62 MET cc_start: 0.9311 (mmp) cc_final: 0.9078 (mmp)
REVERT: R   88 THR cc_start: 0.9130 (m) cc_final: 0.8917 (p)
REVERT: R  113 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8904 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0962
  time to fit residues: 19.9075
Evaluate side-chains
  105 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 88 optimal weight:   10.0000
   chunk 85 optimal weight:    6.9990
   chunk 43 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9980
   chunk 103 optimal weight:    6.9990
   chunk 99 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   overall best weight:    3.1586

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

Flipped N/Q/H residues before XYZ refinement:
** O  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.028782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2546 r_free = 0.2546 target = 0.021179 restraints weight = 173594.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.021955 restraints weight = 84099.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.2612 r_free = 0.2612 target = 0.022469 restraints weight = 51625.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.022836 restraints weight = 36322.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.023095 restraints weight = 28064.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.2630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.3671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  14032  Z= 0.232
  Angle     :  0.630   6.470  20419  Z= 0.378
  Chirality :  0.035   0.158   2320
  Planarity :  0.004   0.063   1398
  Dihedral  : 32.718 177.072   4580
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.55 (0.29), residues: 752
  helix:  1.55 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.24 (0.39), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG N  79 
 TYR   0.037   0.002   TYR R  83 
 PHE   0.019   0.002   PHE K 104 
 HIS   0.005   0.001   HIS P  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 (14032)
  covalent geometry    : angle       0.62966 (20419)
  hydrogen bonds       : bond        0.05562 (  829)
  hydrogen bonds       : angle       3.39122 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9536 (m-10) cc_final: 0.9037 (m-80)
REVERT: K   85 GLN cc_start: 0.9369 (mt0) cc_final: 0.8777 (mt0)
REVERT: K   90 MET cc_start: 0.9159 (mmp) cc_final: 0.8818 (mmp)
REVERT: K   94 GLU cc_start: 0.9398 (mm-30) cc_final: 0.9097 (mm-30)
REVERT: K  120 MET cc_start: 0.8854 (mtm) cc_final: 0.8220 (mtt)
REVERT: L   59 LYS cc_start: 0.9701 (tppt) cc_final: 0.9394 (tppt)
REVERT: L   63 GLU cc_start: 0.9420 (mt-10) cc_final: 0.9097 (mp0)
REVERT: M   41 GLU cc_start: 0.8441 (pm20) cc_final: 0.7906 (tm-30)
REVERT: M   56 GLU cc_start: 0.9335 (mt-10) cc_final: 0.9055 (mt-10)
REVERT: M   78 ILE cc_start: 0.9291 (pt) cc_final: 0.9052 (tp)
REVERT: M   90 ASP cc_start: 0.7169 (t0) cc_final: 0.6666 (t0)
REVERT: N   47 GLN cc_start: 0.9429 (mm-40) cc_final: 0.9172 (mm110)
REVERT: N   59 MET cc_start: 0.8829 (tpt) cc_final: 0.8434 (tpt)
REVERT: N   71 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8689 (mm-30)
REVERT: N  102 LEU cc_start: 0.8755 (tp) cc_final: 0.8434 (tp)
REVERT: N  105 GLU cc_start: 0.9575 (mp0) cc_final: 0.9270 (pm20)
REVERT: N  109 HIS cc_start: 0.9719 (m90) cc_final: 0.9347 (m170)
REVERT: O   76 GLN cc_start: 0.9037 (tp40) cc_final: 0.8790 (mm-40)
REVERT: O   86 SER cc_start: 0.9832 (t) cc_final: 0.9588 (p)
REVERT: O  104 PHE cc_start: 0.9445 (m-80) cc_final: 0.8835 (m-80)
REVERT: R   71 GLU cc_start: 0.9489 (mm-30) cc_final: 0.9267 (mm-30)
REVERT: R   73 ILE cc_start: 0.9680 (mm) cc_final: 0.9448 (mm)
REVERT: R   76 GLU cc_start: 0.9382 (tp30) cc_final: 0.9104 (mt-10)
REVERT: R   88 THR cc_start: 0.9244 (m) cc_final: 0.8968 (p)
REVERT: R  101 LEU cc_start: 0.9273 (tt) cc_final: 0.8826 (tt)
REVERT: R  113 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8952 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.0991
  time to fit residues: 21.6933
Evaluate side-chains
  111 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 103 optimal weight:    6.9990
   chunk 70 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 101 optimal weight:    7.9990
   chunk 105 optimal weight:   10.0000
   chunk 42 optimal weight:    0.6980
   chunk 99 optimal weight:    5.9990
   chunk 94 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   chunk 58 optimal weight:    0.8980
   chunk 76 optimal weight:    6.9990
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.029652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2571 r_free = 0.2571 target = 0.021737 restraints weight = 173101.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.022525 restraints weight = 84743.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.023054 restraints weight = 52528.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.023399 restraints weight = 37030.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.023677 restraints weight = 28922.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.4030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14032  Z= 0.180
  Angle     :  0.602   6.888  20419  Z= 0.360
  Chirality :  0.034   0.150   2320
  Planarity :  0.004   0.063   1398
  Dihedral  : 32.517 179.004   4580
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  1.57 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.30), residues: 752
  helix:  1.80 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.30 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Q  29 
 TYR   0.035   0.002   TYR R  83 
 PHE   0.015   0.002   PHE O 104 
 HIS   0.005   0.001   HIS O  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (14032)
  covalent geometry    : angle       0.60209 (20419)
  hydrogen bonds       : bond        0.04413 (  829)
  hydrogen bonds       : angle       3.21884 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 147
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9553 (m-10) cc_final: 0.9043 (m-80)
REVERT: K   85 GLN cc_start: 0.9332 (mt0) cc_final: 0.8650 (mt0)
REVERT: K   90 MET cc_start: 0.9159 (mmp) cc_final: 0.8609 (mmp)
REVERT: K  104 PHE cc_start: 0.9676 (m-10) cc_final: 0.9378 (m-10)
REVERT: K  120 MET cc_start: 0.8824 (mtm) cc_final: 0.8090 (mtt)
REVERT: K  123 ASP cc_start: 0.9651 (m-30) cc_final: 0.9425 (m-30)
REVERT: L   44 LYS cc_start: 0.8846 (pptt) cc_final: 0.8621 (pptt)
REVERT: L   59 LYS cc_start: 0.9654 (tppt) cc_final: 0.9403 (tppt)
REVERT: L   63 GLU cc_start: 0.9453 (mt-10) cc_final: 0.9178 (mt-10)
REVERT: M   36 LYS cc_start: 0.9577 (mptt) cc_final: 0.9269 (mmtm)
REVERT: M   56 GLU cc_start: 0.9366 (mt-10) cc_final: 0.9077 (mt-10)
REVERT: M   78 ILE cc_start: 0.9330 (pt) cc_final: 0.9099 (tp)
REVERT: M   90 ASP cc_start: 0.6902 (t0) cc_final: 0.6409 (t0)
REVERT: N   47 GLN cc_start: 0.9378 (mm-40) cc_final: 0.9102 (mm110)
REVERT: N   71 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8658 (mm-30)
REVERT: N  102 LEU cc_start: 0.8729 (tp) cc_final: 0.8443 (tp)
REVERT: N  105 GLU cc_start: 0.9590 (mp0) cc_final: 0.9247 (pm20)
REVERT: N  109 HIS cc_start: 0.9703 (m90) cc_final: 0.9324 (m-70)
REVERT: O   86 SER cc_start: 0.9817 (t) cc_final: 0.9325 (p)
REVERT: O   90 MET cc_start: 0.9366 (mmp) cc_final: 0.9018 (mmt)
REVERT: O   93 GLN cc_start: 0.9338 (pt0) cc_final: 0.9035 (pp30)
REVERT: O  104 PHE cc_start: 0.9364 (m-80) cc_final: 0.8737 (m-80)
REVERT: P   58 LEU cc_start: 0.9782 (tt) cc_final: 0.9485 (pp)
REVERT: P   72 TYR cc_start: 0.9360 (m-80) cc_final: 0.8960 (m-80)
REVERT: R   71 GLU cc_start: 0.9486 (mm-30) cc_final: 0.9234 (mm-30)
REVERT: R   76 GLU cc_start: 0.9378 (tp30) cc_final: 0.8836 (mt-10)
REVERT: R  101 LEU cc_start: 0.9272 (tt) cc_final: 0.8846 (tt)
REVERT: R  113 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8955 (mm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 148
  average time/residue: 0.1065
  time to fit residues: 23.2135
Evaluate side-chains
  118 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 90 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 94 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 99 optimal weight:    5.9990
   chunk 102 optimal weight:    8.9990
   chunk 31 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 6 optimal weight:    8.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
** M  84 GLN ** 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 = 0.2878 r_free = 0.2878 target = 0.028886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2552 r_free = 0.2552 target = 0.021253 restraints weight = 173508.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2592 r_free = 0.2592 target = 0.022026 restraints weight = 84823.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2617 r_free = 0.2617 target = 0.022503 restraints weight = 52320.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.022881 restraints weight = 37115.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.023139 restraints weight = 28472.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.2635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.4323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  14032  Z= 0.211
  Angle     :  0.610   6.311  20419  Z= 0.366
  Chirality :  0.034   0.152   2320
  Planarity :  0.004   0.062   1398
  Dihedral  : 32.530 177.980   4580
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.89 %
    Favored  : 97.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.77 (0.30), residues: 752
  helix:  1.78 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.37 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Q  29 
 TYR   0.025   0.002   TYR R  83 
 PHE   0.010   0.001   PHE O 104 
 HIS   0.006   0.001   HIS O  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 (14032)
  covalent geometry    : angle       0.61034 (20419)
  hydrogen bonds       : bond        0.05310 (  829)
  hydrogen bonds       : angle       3.36063 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9554 (m-10) cc_final: 0.8990 (m-80)
REVERT: K   59 GLU cc_start: 0.8955 (pm20) cc_final: 0.8751 (pm20)
REVERT: K   90 MET cc_start: 0.9239 (mmp) cc_final: 0.8891 (mmp)
REVERT: K  104 PHE cc_start: 0.9642 (m-10) cc_final: 0.9337 (m-10)
REVERT: K  120 MET cc_start: 0.8911 (mtm) cc_final: 0.8065 (mtt)
REVERT: L   59 LYS cc_start: 0.9668 (tppt) cc_final: 0.9458 (tppt)
REVERT: L   63 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9114 (pt0)
REVERT: L   75 HIS cc_start: 0.9159 (t70) cc_final: 0.8771 (t70)
REVERT: M   36 LYS cc_start: 0.9554 (mptt) cc_final: 0.9267 (mmtm)
REVERT: M   41 GLU cc_start: 0.9115 (mp0) cc_final: 0.7977 (tp30)
REVERT: M   56 GLU cc_start: 0.9338 (mt-10) cc_final: 0.9043 (mt-10)
REVERT: M   78 ILE cc_start: 0.9298 (pt) cc_final: 0.9049 (tp)
REVERT: M   90 ASP cc_start: 0.6923 (t0) cc_final: 0.6432 (t0)
REVERT: N   47 GLN cc_start: 0.9376 (mm-40) cc_final: 0.9104 (mm110)
REVERT: N   71 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8631 (mm-30)
REVERT: N   96 THR cc_start: 0.9723 (m) cc_final: 0.9475 (p)
REVERT: N   99 ARG cc_start: 0.9281 (mtp85) cc_final: 0.9070 (mtp-110)
REVERT: N  102 LEU cc_start: 0.8714 (tp) cc_final: 0.8419 (tp)
REVERT: N  105 GLU cc_start: 0.9607 (mp0) cc_final: 0.9204 (pm20)
REVERT: N  109 HIS cc_start: 0.9696 (m90) cc_final: 0.9450 (m170)
REVERT: O   94 GLU cc_start: 0.9505 (mp0) cc_final: 0.9161 (mp0)
REVERT: O  100 LEU cc_start: 0.9705 (mm) cc_final: 0.9487 (mt)
REVERT: O  104 PHE cc_start: 0.9393 (m-80) cc_final: 0.8832 (m-80)
REVERT: R  113 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8905 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1005
  time to fit residues: 21.7001
Evaluate side-chains
  115 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 76 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 70 optimal weight:    0.2980
   chunk 9 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 11 optimal weight:    8.9990
   chunk 88 optimal weight:   10.0000
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  95 GLN
O  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.029613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.021937 restraints weight = 171472.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.022740 restraints weight = 82796.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.023260 restraints weight = 50495.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.023623 restraints weight = 35479.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.023850 restraints weight = 27458.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.4531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  14032  Z= 0.171
  Angle     :  0.591   6.186  20419  Z= 0.355
  Chirality :  0.034   0.165   2320
  Planarity :  0.004   0.062   1398
  Dihedral  : 32.393 179.108   4580
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.30), residues: 752
  helix:  1.73 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.37 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Q  29 
 TYR   0.022   0.001   TYR R  83 
 PHE   0.021   0.002   PHE M  25 
 HIS   0.005   0.001   HIS L  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (14032)
  covalent geometry    : angle       0.59120 (20419)
  hydrogen bonds       : bond        0.04103 (  829)
  hydrogen bonds       : angle       3.30148 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9501 (m-10) cc_final: 0.8917 (m-80)
REVERT: K   85 GLN cc_start: 0.9446 (mt0) cc_final: 0.9007 (mt0)
REVERT: K  120 MET cc_start: 0.8893 (mtm) cc_final: 0.8109 (mtt)
REVERT: K  123 ASP cc_start: 0.9646 (m-30) cc_final: 0.9446 (m-30)
REVERT: L   59 LYS cc_start: 0.9640 (tppt) cc_final: 0.9418 (tppt)
REVERT: L   63 GLU cc_start: 0.9470 (mt-10) cc_final: 0.9111 (pt0)
REVERT: M   36 LYS cc_start: 0.9574 (mptt) cc_final: 0.9289 (mmtm)
REVERT: M   56 GLU cc_start: 0.9470 (mt-10) cc_final: 0.9217 (mt-10)
REVERT: M   90 ASP cc_start: 0.7001 (t0) cc_final: 0.6531 (t0)
REVERT: N   59 MET cc_start: 0.9129 (tpp) cc_final: 0.8870 (tpt)
REVERT: N   71 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8564 (mm-30)
REVERT: N   99 ARG cc_start: 0.9259 (mtp85) cc_final: 0.9049 (mtp-110)
REVERT: N  102 LEU cc_start: 0.8640 (tp) cc_final: 0.8371 (tp)
REVERT: N  105 GLU cc_start: 0.9605 (mp0) cc_final: 0.9169 (pm20)
REVERT: N  109 HIS cc_start: 0.9766 (m90) cc_final: 0.9398 (m-70)
REVERT: O   93 GLN cc_start: 0.9491 (pt0) cc_final: 0.8979 (pp30)
REVERT: O  100 LEU cc_start: 0.9745 (mm) cc_final: 0.9526 (mm)
REVERT: O  104 PHE cc_start: 0.9367 (m-80) cc_final: 0.8775 (m-80)
REVERT: O  120 MET cc_start: 0.8535 (mtt) cc_final: 0.8191 (mtt)
REVERT: P   91 LYS cc_start: 0.9472 (tmmt) cc_final: 0.9032 (pttp)
REVERT: R   62 MET cc_start: 0.9306 (mmp) cc_final: 0.9053 (mmp)
REVERT: R   71 GLU cc_start: 0.9501 (mm-30) cc_final: 0.9245 (mm-30)
REVERT: R   83 TYR cc_start: 0.8643 (m-80) cc_final: 0.8242 (m-80)
REVERT: R  113 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8933 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1066
  time to fit residues: 23.4848
Evaluate side-chains
  118 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 98 optimal weight:    7.9990
   chunk 87 optimal weight:    7.9990
   chunk 27 optimal weight:    0.0470
   chunk 44 optimal weight:    5.9990
   chunk 74 optimal weight:    8.9990
   chunk 97 optimal weight:    6.9990
   chunk 92 optimal weight:    6.9990
   chunk 85 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    2.7684

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

Flipped N/Q/H residues before XYZ refinement:
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** 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 = 0.2905 r_free = 0.2905 target = 0.032247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.025546 restraints weight = 191414.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.026334 restraints weight = 88668.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.026884 restraints weight = 52597.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 61)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.027330 restraints weight = 35222.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.027622 restraints weight = 26235.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.4757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  14032  Z= 0.220
  Angle     :  0.615   6.665  20419  Z= 0.368
  Chirality :  0.035   0.163   2320
  Planarity :  0.004   0.059   1398
  Dihedral  : 32.457 178.326   4580
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.66 (0.30), residues: 752
  helix:  1.69 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.36 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Q  29 
 TYR   0.030   0.002   TYR M  50 
 PHE   0.030   0.002   PHE K 104 
 HIS   0.011   0.001   HIS L  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 (14032)
  covalent geometry    : angle       0.61544 (20419)
  hydrogen bonds       : bond        0.05628 (  829)
  hydrogen bonds       : angle       3.43381 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9479 (m-10) cc_final: 0.8815 (m-80)
REVERT: K   85 GLN cc_start: 0.9413 (mt0) cc_final: 0.8869 (mt0)
REVERT: K   90 MET cc_start: 0.9311 (mmp) cc_final: 0.8809 (mmp)
REVERT: K   94 GLU cc_start: 0.9589 (mm-30) cc_final: 0.9167 (mm-30)
REVERT: K  120 MET cc_start: 0.8834 (mtm) cc_final: 0.8070 (mtt)
REVERT: M   36 LYS cc_start: 0.9542 (mptt) cc_final: 0.9244 (mmtm)
REVERT: M   41 GLU cc_start: 0.9073 (mp0) cc_final: 0.8148 (tp30)
REVERT: M   79 ILE cc_start: 0.9536 (tp) cc_final: 0.9218 (pt)
REVERT: M   90 ASP cc_start: 0.6903 (t0) cc_final: 0.6459 (t0)
REVERT: N   30 LYS cc_start: 0.4984 (tptt) cc_final: 0.4705 (mmmt)
REVERT: N   71 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8583 (mm-30)
REVERT: N  102 LEU cc_start: 0.8669 (tp) cc_final: 0.8348 (tp)
REVERT: N  105 GLU cc_start: 0.9649 (mp0) cc_final: 0.9171 (pm20)
REVERT: N  109 HIS cc_start: 0.9767 (m90) cc_final: 0.9425 (m-70)
REVERT: O   93 GLN cc_start: 0.9403 (pt0) cc_final: 0.9081 (pp30)
REVERT: O  104 PHE cc_start: 0.9356 (m-80) cc_final: 0.8750 (m-80)
REVERT: O  120 MET cc_start: 0.8333 (mtt) cc_final: 0.7970 (mtt)
REVERT: P   91 LYS cc_start: 0.9440 (tmmt) cc_final: 0.9013 (pttp)
REVERT: R   62 MET cc_start: 0.9378 (mmp) cc_final: 0.9130 (mmp)
REVERT: R   71 GLU cc_start: 0.9504 (mm-30) cc_final: 0.9248 (mm-30)
REVERT: R   83 TYR cc_start: 0.8753 (m-80) cc_final: 0.8317 (m-80)
REVERT: R  113 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8969 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1060
  time to fit residues: 23.0579
Evaluate side-chains
  109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   chunk 101 optimal weight:    7.9990
   chunk 79 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 45 optimal weight:    8.9990
   chunk 41 optimal weight:    0.7980
   chunk 11 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  75 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 = 0.2861 r_free = 0.2861 target = 0.028246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2546 r_free = 0.2546 target = 0.020948 restraints weight = 178284.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2586 r_free = 0.2586 target = 0.021720 restraints weight = 85023.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2612 r_free = 0.2612 target = 0.022224 restraints weight = 51649.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.022606 restraints weight = 36268.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.022854 restraints weight = 27831.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.5070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  14032  Z= 0.227
  Angle     :  0.634   7.083  20419  Z= 0.378
  Chirality :  0.035   0.160   2320
  Planarity :  0.004   0.060   1398
  Dihedral  : 32.517 177.572   4580
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.31), residues: 752
  helix:  1.63 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.41 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Q  29 
 TYR   0.025   0.002   TYR R  83 
 PHE   0.029   0.002   PHE K 104 
 HIS   0.009   0.001   HIS L  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 (14032)
  covalent geometry    : angle       0.63367 (20419)
  hydrogen bonds       : bond        0.05655 (  829)
  hydrogen bonds       : angle       3.54400 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9503 (m-10) cc_final: 0.8927 (m-80)
REVERT: K   59 GLU cc_start: 0.8972 (pm20) cc_final: 0.8745 (pm20)
REVERT: K   85 GLN cc_start: 0.9455 (mt0) cc_final: 0.8944 (mt0)
REVERT: K   90 MET cc_start: 0.9281 (mmp) cc_final: 0.8910 (mmp)
REVERT: K   94 GLU cc_start: 0.9525 (mm-30) cc_final: 0.9136 (mm-30)
REVERT: K  120 MET cc_start: 0.8871 (mtm) cc_final: 0.8089 (mtt)
REVERT: L   63 GLU cc_start: 0.9385 (mt-10) cc_final: 0.9159 (mt-10)
REVERT: M   36 LYS cc_start: 0.9552 (mptt) cc_final: 0.9260 (mmtm)
REVERT: M   41 GLU cc_start: 0.9048 (mp0) cc_final: 0.8211 (tp30)
REVERT: M   90 ASP cc_start: 0.6938 (t0) cc_final: 0.6486 (t0)
REVERT: N   59 MET cc_start: 0.8989 (tpp) cc_final: 0.8768 (tpt)
REVERT: N   71 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8646 (mm-30)
REVERT: N  102 LEU cc_start: 0.8842 (tp) cc_final: 0.8493 (tp)
REVERT: N  105 GLU cc_start: 0.9666 (mp0) cc_final: 0.9193 (pm20)
REVERT: N  109 HIS cc_start: 0.9725 (m90) cc_final: 0.9396 (m-70)
REVERT: O   94 GLU cc_start: 0.9542 (mp0) cc_final: 0.9323 (mp0)
REVERT: O  104 PHE cc_start: 0.9442 (m-80) cc_final: 0.8802 (m-80)
REVERT: O  120 MET cc_start: 0.8455 (mtt) cc_final: 0.8068 (mtt)
REVERT: P   91 LYS cc_start: 0.9482 (tmmt) cc_final: 0.9028 (pttm)
REVERT: R   62 MET cc_start: 0.9350 (mmp) cc_final: 0.9089 (mmp)
REVERT: R   71 GLU cc_start: 0.9489 (mm-30) cc_final: 0.9262 (mm-30)
REVERT: R  113 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8972 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1028
  time to fit residues: 22.2898
Evaluate side-chains
  109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 86 optimal weight:    7.9990
   chunk 85 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 98 optimal weight:    7.9990
   chunk 95 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  75 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 = 0.2846 r_free = 0.2846 target = 0.027960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2534 r_free = 0.2534 target = 0.020794 restraints weight = 179160.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2575 r_free = 0.2575 target = 0.021565 restraints weight = 84954.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.022082 restraints weight = 51732.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.2619 r_free = 0.2619 target = 0.022454 restraints weight = 36207.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.022683 restraints weight = 27757.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.5353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  14032  Z= 0.228
  Angle     :  0.634   7.165  20419  Z= 0.378
  Chirality :  0.036   0.193   2320
  Planarity :  0.005   0.057   1398
  Dihedral  : 32.499 177.855   4580
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.30), residues: 752
  helix:  1.55 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.43 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  92 
 TYR   0.031   0.002   TYR R  83 
 PHE   0.027   0.002   PHE K 104 
 HIS   0.007   0.002   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (14032)
  covalent geometry    : angle       0.63446 (20419)
  hydrogen bonds       : bond        0.05748 (  829)
  hydrogen bonds       : angle       3.57183 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9508 (m-10) cc_final: 0.8911 (m-80)
REVERT: K   59 GLU cc_start: 0.8997 (pm20) cc_final: 0.8786 (pm20)
REVERT: K   85 GLN cc_start: 0.9447 (mt0) cc_final: 0.8953 (mt0)
REVERT: K   90 MET cc_start: 0.9262 (mmp) cc_final: 0.8895 (mmp)
REVERT: K   94 GLU cc_start: 0.9512 (mm-30) cc_final: 0.9130 (mm-30)
REVERT: K  120 MET cc_start: 0.8826 (mtm) cc_final: 0.8106 (mtt)
REVERT: L   58 LEU cc_start: 0.9781 (tt) cc_final: 0.9554 (pp)
REVERT: L   63 GLU cc_start: 0.9405 (mt-10) cc_final: 0.9156 (mt-10)
REVERT: L   74 GLU cc_start: 0.9571 (tp30) cc_final: 0.9286 (mp0)
REVERT: L   75 HIS cc_start: 0.9285 (t70) cc_final: 0.8984 (t70)
REVERT: M   36 LYS cc_start: 0.9553 (mptt) cc_final: 0.9276 (mmtm)
REVERT: M   41 GLU cc_start: 0.8946 (mp0) cc_final: 0.8260 (tp30)
REVERT: M   79 ILE cc_start: 0.9562 (tp) cc_final: 0.9242 (pt)
REVERT: M   90 ASP cc_start: 0.6942 (t0) cc_final: 0.6579 (t0)
REVERT: N   59 MET cc_start: 0.9068 (tpp) cc_final: 0.8795 (tpt)
REVERT: N   71 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8646 (mm-30)
REVERT: N   99 ARG cc_start: 0.9395 (mmm-85) cc_final: 0.9165 (mmm-85)
REVERT: N  102 LEU cc_start: 0.8704 (tp) cc_final: 0.8366 (tp)
REVERT: N  105 GLU cc_start: 0.9659 (mp0) cc_final: 0.9141 (pm20)
REVERT: N  109 HIS cc_start: 0.9701 (m90) cc_final: 0.9319 (m-70)
REVERT: O  104 PHE cc_start: 0.9462 (m-80) cc_final: 0.8820 (m-80)
REVERT: P   91 LYS cc_start: 0.9481 (tmmt) cc_final: 0.9002 (pttm)
REVERT: R   71 GLU cc_start: 0.9471 (mm-30) cc_final: 0.9255 (mm-30)
REVERT: R   83 TYR cc_start: 0.8688 (m-80) cc_final: 0.8312 (m-80)
REVERT: R  113 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8985 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1148
  time to fit residues: 23.7295
Evaluate side-chains
  109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 53 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9990
   chunk 96 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  63 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 = 0.2871 r_free = 0.2871 target = 0.028733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2566 r_free = 0.2566 target = 0.021552 restraints weight = 173862.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.022344 restraints weight = 82386.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.022867 restraints weight = 49916.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.023253 restraints weight = 34865.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.023471 restraints weight = 26569.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.5462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  14032  Z= 0.180
  Angle     :  0.624   6.844  20419  Z= 0.370
  Chirality :  0.035   0.184   2320
  Planarity :  0.004   0.057   1398
  Dihedral  : 32.377 178.532   4580
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.58 (0.31), residues: 752
  helix:  1.63 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.42 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Q  29 
 TYR   0.024   0.002   TYR R  83 
 PHE   0.029   0.002   PHE K 104 
 HIS   0.005   0.001   HIS L  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (14032)
  covalent geometry    : angle       0.62360 (20419)
  hydrogen bonds       : bond        0.04615 (  829)
  hydrogen bonds       : angle       3.47409 ( 2037)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1758.46 seconds
wall clock time: 31 minutes 12.69 seconds (1872.69 seconds total)