Starting phenix.real_space_refine
on Fri Aug 22 16:37:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8equ_28546/08_2025/8equ_28546_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8equ_28546/08_2025/8equ_28546.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8equ_28546/08_2025/8equ_28546.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8equ_28546/08_2025/8equ_28546.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8equ_28546/08_2025/8equ_28546_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8equ_28546/08_2025/8equ_28546_neut.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      32      5.16       5
     C    3680      2.51       5
     N     976      2.21       5
     O    1074      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5764
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 191, 1563
          Classifications: {'peptide': 191}
          Link IDs: {'PTRANS': 4, 'TRANS': 186}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 506
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 506
          Classifications: {'peptide': 80}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 5, 'TRANS': 74}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 105
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 88
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 5, 'TYR:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 51
    Chain: "D"
      Number of atoms: 395
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 395
          Classifications: {'peptide': 79}
          Incomplete info: {'truncation_to_alanine': 79}
          Link IDs: {'TRANS': 78}
          Unresolved non-hydrogen bonds: 158
          Unresolved non-hydrogen angles: 237
          Unresolved non-hydrogen dihedrals: 79
          Planarities with less than four sites: {'UNK:plan-1': 79}
          Unresolved non-hydrogen planarities: 79
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'PEE': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 28
  Restraints were copied for chains:
    B, F, E, G, H
  Time building chain proxies: 1.69, per 1000 atoms: 0.29
  Number of scatterers: 5764
  At special positions: 0
  Unit cell: (90.308, 93.684, 89.464, 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      32     16.00
     P       2     15.00
     O    1074      8.00
     N     976      7.00
     C    3680      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 183.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1668

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 2 sheets defined
      111.8% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 61
      removed outlier: 3.529A  pdb=" N   ILE A  47 " --> pdb=" O   PHE A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 99
    Processing helix  chain 'A' and resid 105 through 134
    Processing helix  chain 'A' and resid 136 through 141
    Processing helix  chain 'B' and resid 43 through 61
      removed outlier: 3.528A  pdb=" N   ILE B  47 " --> pdb=" O   PHE B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 99
    Processing helix  chain 'B' and resid 105 through 134
    Processing helix  chain 'B' and resid 136 through 141
    Processing helix  chain 'C' and resid 2 through 19
      removed outlier: 3.502A  pdb=" N   ILE C   6 " --> pdb=" O   LEU C   2 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 37
      removed outlier: 3.911A  pdb=" N   GLU C  24 " --> pdb=" O   ASP C  20 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   CYS C  35 " --> pdb=" O   LEU C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 67
      removed outlier: 4.298A  pdb=" N   ASP C  52 " --> pdb=" O   LYS C  48 " (cutoff:3.500A)
      Proline residue:  C  56  - end of helix
    Processing helix  chain 'C' and resid 68 through 76
      removed outlier: 3.561A  pdb=" N   LEU C  76 " --> pdb=" O   VAL C  72 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 19
    Processing helix  chain 'D' and resid 20 through 36
      removed outlier: 3.872A  pdb=" N   UNK D  24 " --> pdb=" O   UNK D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 67
      removed outlier: 4.055A  pdb=" N   UNK D  46 " --> pdb=" O   UNK D  42 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   UNK D  56 " --> pdb=" O   UNK D  52 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   UNK D  57 " --> pdb=" O   UNK D  53 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 76
    Processing helix  chain 'E' and resid 2 through 19
    Processing helix  chain 'E' and resid 20 through 36
      removed outlier: 3.874A  pdb=" N   UNK E  24 " --> pdb=" O   UNK E  20 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 40 through 67
      removed outlier: 4.055A  pdb=" N   UNK E  46 " --> pdb=" O   UNK E  42 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   UNK E  56 " --> pdb=" O   UNK E  52 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   UNK E  57 " --> pdb=" O   UNK E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 68 through 76
    Processing helix  chain 'F' and resid 2 through 19
      removed outlier: 3.501A  pdb=" N   ILE F   6 " --> pdb=" O   LEU F   2 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 20 through 37
      removed outlier: 3.911A  pdb=" N   GLU F  24 " --> pdb=" O   ASP F  20 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   CYS F  35 " --> pdb=" O   LEU F  31 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 42 through 67
      removed outlier: 4.298A  pdb=" N   ASP F  52 " --> pdb=" O   LYS F  48 " (cutoff:3.500A)
      Proline residue:  F  56  - end of helix
    Processing helix  chain 'F' and resid 68 through 76
      removed outlier: 3.560A  pdb=" N   LEU F  76 " --> pdb=" O   VAL F  72 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 2 through 19
    Processing helix  chain 'G' and resid 20 through 36
      removed outlier: 3.873A  pdb=" N   UNK G  24 " --> pdb=" O   UNK G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 40 through 67
      removed outlier: 4.055A  pdb=" N   UNK G  46 " --> pdb=" O   UNK G  42 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   UNK G  56 " --> pdb=" O   UNK G  52 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   UNK G  57 " --> pdb=" O   UNK G  53 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 68 through 76
    Processing helix  chain 'H' and resid 2 through 19
    Processing helix  chain 'H' and resid 20 through 36
      removed outlier: 3.874A  pdb=" N   UNK H  24 " --> pdb=" O   UNK H  20 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 40 through 67
      removed outlier: 4.055A  pdb=" N   UNK H  46 " --> pdb=" O   UNK H  42 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   UNK H  56 " --> pdb=" O   UNK H  52 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   UNK H  57 " --> pdb=" O   UNK H  53 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 68 through 76
    Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 160
      removed outlier: 6.193A  pdb=" N   HIS A 150 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 8.447A  pdb=" N   CYS A 200 " --> pdb=" O   HIS A 150 " (cutoff:3.500A)
      removed outlier: 5.514A  pdb=" N   LEU A 214 " --> pdb=" O   ASN A 234 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ASN A 234 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER A 216 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 155 through 160
      removed outlier: 6.194A  pdb=" N   HIS B 150 " --> pdb=" O   CYS B 200 " (cutoff:3.500A)
      removed outlier: 8.447A  pdb=" N   CYS B 200 " --> pdb=" O   HIS B 150 " (cutoff:3.500A)
      removed outlier: 5.514A  pdb=" N   LEU B 214 " --> pdb=" O   ASN B 234 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ASN B 234 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   SER B 216 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)

    506 hydrogen bonds defined for protein.
    1500 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.05

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 966
        1.32 -     1.44: 1530
        1.44 -     1.57: 3320
        1.57 -     1.70: 4
        1.70 -     1.82: 38
  Bond restraints: 5858
  Sorted by residual:
  bond pdb=" C10 PEE B 401 "
       pdb=" O2  PEE B 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.429 -0.097 2.00e-02 2.50e+03 2.34e+01
  bond pdb=" C10 PEE A 401 "
       pdb=" O2  PEE A 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.428 -0.096 2.00e-02 2.50e+03 2.29e+01
  bond pdb=" C30 PEE A 401 "
       pdb=" O3  PEE A 401 "
    ideal  model  delta    sigma   weight residual
    1.327  1.411 -0.084 2.00e-02 2.50e+03 1.77e+01
  bond pdb=" C30 PEE B 401 "
       pdb=" O3  PEE B 401 "
    ideal  model  delta    sigma   weight residual
    1.327  1.411 -0.084 2.00e-02 2.50e+03 1.75e+01
  bond pdb=" C   LEU A  41 "
       pdb=" N   PRO A  42 "
    ideal  model  delta    sigma   weight residual
    1.333  1.358 -0.025 1.01e-02 9.80e+03 5.99e+00
  ... (remaining 5853 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.29: 7999
        3.29 -     6.57: 29
        6.57 -     9.86: 10
        9.86 -    13.15: 0
       13.15 -    16.44: 2
  Bond angle restraints: 8040
  Sorted by residual:
  angle pdb=" O3P PEE B 401 "
        pdb=" P   PEE B 401 "
        pdb=" O4P PEE B 401 "
      ideal   model   delta    sigma   weight residual
      92.91  109.35  -16.44 3.00e+00 1.11e-01 3.00e+01
  angle pdb=" O3P PEE A 401 "
        pdb=" P   PEE A 401 "
        pdb=" O4P PEE A 401 "
      ideal   model   delta    sigma   weight residual
      92.91  109.31  -16.40 3.00e+00 1.11e-01 2.99e+01
  angle pdb=" CB  MET A 125 "
        pdb=" CG  MET A 125 "
        pdb=" SD  MET A 125 "
      ideal   model   delta    sigma   weight residual
     112.70  122.43   -9.73 3.00e+00 1.11e-01 1.05e+01
  angle pdb=" CB  MET B 125 "
        pdb=" CG  MET B 125 "
        pdb=" SD  MET B 125 "
      ideal   model   delta    sigma   weight residual
     112.70  122.40   -9.70 3.00e+00 1.11e-01 1.05e+01
  angle pdb=" O1P PEE A 401 "
        pdb=" P   PEE A 401 "
        pdb=" O2P PEE A 401 "
      ideal   model   delta    sigma   weight residual
     119.43  109.80    9.63 3.00e+00 1.11e-01 1.03e+01
  ... (remaining 8035 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.18: 3355
       28.18 -    56.37: 57
       56.37 -    84.55: 16
       84.55 -   112.73: 0
      112.73 -   140.91: 4
  Dihedral angle restraints: 3432
    sinusoidal: 882
      harmonic: 2550
  Sorted by residual:
  dihedral pdb=" CA  HIS A 204 "
           pdb=" C   HIS A 204 "
           pdb=" N   SER A 205 "
           pdb=" CA  SER A 205 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.40   26.60     0      5.00e+00 4.00e-02 2.83e+01
  dihedral pdb=" CA  HIS B 204 "
           pdb=" C   HIS B 204 "
           pdb=" N   SER B 205 "
           pdb=" CA  SER B 205 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.42   26.58     0      5.00e+00 4.00e-02 2.83e+01
  dihedral pdb=" C3  PEE B 401 "
           pdb=" C1  PEE B 401 "
           pdb=" C2  PEE B 401 "
           pdb=" O3P PEE B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.73  -78.18  140.91     1      3.00e+01 1.11e-03 1.89e+01
  ... (remaining 3429 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 821
       0.048 -    0.096: 159
       0.096 -    0.144: 20
       0.144 -    0.193: 0
       0.193 -    0.241: 2
  Chirality restraints: 1002
  Sorted by residual:
  chirality pdb=" C2  PEE A 401 "
            pdb=" C1  PEE A 401 "
            pdb=" C3  PEE A 401 "
            pdb=" O2  PEE A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.57    0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" C2  PEE B 401 "
            pdb=" C1  PEE B 401 "
            pdb=" C3  PEE B 401 "
            pdb=" O2  PEE B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.57    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CA  ILE A 169 "
            pdb=" N   ILE A 169 "
            pdb=" C   ILE A 169 "
            pdb=" CB  ILE A 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.70e-01
  ... (remaining 999 not shown)

  Planarity restraints: 1022
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B  41 "   -0.011 2.00e-02 2.50e+03   2.13e-02 4.54e+00
        pdb=" C   LEU B  41 "    0.037 2.00e-02 2.50e+03
        pdb=" O   LEU B  41 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   PRO B  42 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  41 "   -0.011 2.00e-02 2.50e+03   2.13e-02 4.53e+00
        pdb=" C   LEU A  41 "    0.037 2.00e-02 2.50e+03
        pdb=" O   LEU A  41 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   PRO A  42 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 206 "    0.011 2.00e-02 2.50e+03   1.13e-02 2.55e+00
        pdb=" CG  TYR B 206 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 206 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 206 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 206 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 206 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 206 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 206 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1019 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 26
        2.60 -     3.18: 5149
        3.18 -     3.75: 9351
        3.75 -     4.33: 11343
        4.33 -     4.90: 19003
  Nonbonded interactions: 44872
  Sorted by model distance:
  nonbonded pdb=" SG  CYS C  35 "
            pdb=" SG  CYS C  47 "
     model   vdw
     2.025 3.760
  nonbonded pdb=" SG  CYS F  35 "
            pdb=" SG  CYS F  47 "
     model   vdw
     2.026 3.760
  nonbonded pdb=" SG  CYS C   7 "
            pdb=" SG  CYS C  73 "
     model   vdw
     2.031 3.760
  nonbonded pdb=" SG  CYS C   4 "
            pdb=" SG  CYS C  79 "
     model   vdw
     2.032 3.760
  nonbonded pdb=" SG  CYS F   7 "
            pdb=" SG  CYS F  73 "
     model   vdw
     2.032 3.760
  ... (remaining 44867 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.840
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
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      :  0.004   0.097   5858  Z= 0.243
  Angle     :  0.790  16.435   8040  Z= 0.382
  Chirality :  0.040   0.241   1002
  Planarity :  0.004   0.032   1022
  Dihedral  : 14.512 140.915   1764
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  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 aren not related in a simple way.
  whole: -0.12 (0.36), residues: 530
  helix:  0.76 (0.30), residues: 308
  sheet: -0.26 (0.51), residues: 92
  loop : -1.82 (0.49), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  68 
 TYR   0.028   0.002   TYR B 206 
 PHE   0.010   0.001   PHE B  56 
 TRP   0.011   0.002   TRP A 193 
 HIS   0.004   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 5858)
  covalent geometry    : angle       0.79017 ( 8040)
  hydrogen bonds       : bond        0.12579 (  506)
  hydrogen bonds       : angle       5.53053 ( 1500)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 ARG cc_start: 0.7786 (mpp80) cc_final: 0.7553 (mpp80)
REVERT: A  198 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7624 (mmmm)
REVERT: A  210 ASP cc_start: 0.8189 (m-30) cc_final: 0.7947 (m-30)
REVERT: A  213 GLN cc_start: 0.7923 (tt0) cc_final: 0.7377 (tp40)
REVERT: B  198 LYS cc_start: 0.7917 (mtpt) cc_final: 0.7628 (mmmm)
REVERT: B  210 ASP cc_start: 0.8185 (m-30) cc_final: 0.7924 (m-30)
REVERT: B  211 TYR cc_start: 0.8528 (m-80) cc_final: 0.8273 (m-80)
REVERT: B  213 GLN cc_start: 0.7932 (tt0) cc_final: 0.7353 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.4719
  time to fit residues: 49.2900
Evaluate side-chains
  75 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:   30.0000
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:   20.0000
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.1980
   chunk 74 optimal weight:   20.0000
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A  82 ASN
A  93 HIS
** B  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  82 ASN
B  93 HIS
F  77 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.188516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.110736 restraints weight = 7094.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 2.52
r_work: 0.3011 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050   5858  Z= 0.286
  Angle     :  0.606   7.459   8040  Z= 0.304
  Chirality :  0.040   0.151   1002
  Planarity :  0.004   0.039   1022
  Dihedral  :  9.907 102.412    928
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 10.51 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.36), residues: 530
  helix:  1.36 (0.29), residues: 318
  sheet: -0.72 (0.50), residues: 90
  loop : -1.68 (0.52), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 126 
 TYR   0.026   0.002   TYR B 215 
 PHE   0.026   0.003   PHE A  43 
 TRP   0.009   0.002   TRP A 149 
 HIS   0.003   0.001   HIS B  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00680 ( 5858)
  covalent geometry    : angle       0.60558 ( 8040)
  hydrogen bonds       : bond        0.03193 (  506)
  hydrogen bonds       : angle       4.03876 ( 1500)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 TRP cc_start: 0.8493 (t60) cc_final: 0.8176 (t60)
REVERT: A  198 LYS cc_start: 0.8510 (mtpt) cc_final: 0.8194 (mmmm)
REVERT: A  213 GLN cc_start: 0.8652 (tt0) cc_final: 0.8424 (tt0)
REVERT: B  128 TRP cc_start: 0.8504 (t60) cc_final: 0.8194 (t60)
REVERT: B  198 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8162 (mmmm)
REVERT: B  213 GLN cc_start: 0.8639 (tt0) cc_final: 0.8415 (tt0)
REVERT: C    9 ASP cc_start: 0.8644 (m-30) cc_final: 0.8392 (m-30)
  outliers start: 9
  outliers final: 3
  residues processed: 86
  average time/residue: 0.4988
  time to fit residues: 45.1919
Evaluate side-chains
  77 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ARG
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain B residue  222 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 54 optimal weight:   20.0000
   chunk 67 optimal weight:    0.7980
   chunk 74 optimal weight:   20.0000
   chunk 36 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 42 optimal weight:   20.0000
   chunk 61 optimal weight:    0.3980
   chunk 43 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  57 GLN
A  70 GLN
A  78 HIS
B  57 GLN
B  70 GLN
B  78 HIS
F  77 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.190457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.113889 restraints weight = 7044.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.50
r_work: 0.3059 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5858  Z= 0.134
  Angle     :  0.508   7.250   8040  Z= 0.251
  Chirality :  0.035   0.136   1002
  Planarity :  0.003   0.039   1022
  Dihedral  :  9.150  95.925    928
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 15.89 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.36), residues: 530
  helix:  1.66 (0.29), residues: 318
  sheet: -0.72 (0.51), residues: 90
  loop : -1.75 (0.51), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  68 
 TYR   0.009   0.001   TYR A 215 
 PHE   0.010   0.002   PHE B  43 
 TRP   0.009   0.002   TRP A 149 
 HIS   0.002   0.001   HIS B  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 5858)
  covalent geometry    : angle       0.50795 ( 8040)
  hydrogen bonds       : bond        0.02640 (  506)
  hydrogen bonds       : angle       3.68138 ( 1500)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A  128 TRP cc_start: 0.8336 (t60) cc_final: 0.8060 (t60)
REVERT: A  198 LYS cc_start: 0.8522 (mtpt) cc_final: 0.8191 (mmmm)
REVERT: A  213 GLN cc_start: 0.8480 (tt0) cc_final: 0.7992 (tp40)
REVERT: B  128 TRP cc_start: 0.8344 (t60) cc_final: 0.8072 (t60)
REVERT: B  198 LYS cc_start: 0.8517 (mtpt) cc_final: 0.8186 (mmmm)
REVERT: B  213 GLN cc_start: 0.8467 (tt0) cc_final: 0.8182 (tt0)
REVERT: C    9 ASP cc_start: 0.8532 (m-30) cc_final: 0.8267 (m-30)
  outliers start: 4
  outliers final: 2
  residues processed: 89
  average time/residue: 0.4132
  time to fit residues: 38.9016
Evaluate side-chains
  79 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain B residue  222 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 43 optimal weight:    0.4980
   chunk 39 optimal weight:    0.2980
   chunk 25 optimal weight:    0.2980
   chunk 31 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0770
   chunk 56 optimal weight:   20.0000
   chunk 0 optimal weight:    3.9990
   chunk 66 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.3938

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

Flipped N/Q/H residues before XYZ refinement:
F  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.192535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.116321 restraints weight = 7091.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.50
r_work: 0.3090 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5858  Z= 0.105
  Angle     :  0.495   7.489   8040  Z= 0.243
  Chirality :  0.034   0.142   1002
  Planarity :  0.003   0.037   1022
  Dihedral  :  8.509  87.095    928
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 17.76 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.37), residues: 530
  helix:  1.81 (0.29), residues: 316
  sheet: -0.80 (0.53), residues: 90
  loop : -2.00 (0.49), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  68 
 TYR   0.009   0.001   TYR A 154 
 PHE   0.009   0.001   PHE B  43 
 TRP   0.011   0.002   TRP B 131 
 HIS   0.002   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 5858)
  covalent geometry    : angle       0.49498 ( 8040)
  hydrogen bonds       : bond        0.02350 (  506)
  hydrogen bonds       : angle       3.51918 ( 1500)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 87
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A  128 TRP cc_start: 0.8326 (t60) cc_final: 0.8013 (t60)
REVERT: A  155 ASP cc_start: 0.8281 (m-30) cc_final: 0.7802 (m-30)
REVERT: A  198 LYS cc_start: 0.8544 (mtpt) cc_final: 0.8198 (mmmm)
REVERT: A  213 GLN cc_start: 0.8529 (tt0) cc_final: 0.8261 (tt0)
REVERT: B  128 TRP cc_start: 0.8346 (t60) cc_final: 0.8024 (t60)
REVERT: B  155 ASP cc_start: 0.8283 (m-30) cc_final: 0.7718 (m-30)
REVERT: B  198 LYS cc_start: 0.8558 (mtpt) cc_final: 0.8219 (mmmm)
REVERT: B  213 GLN cc_start: 0.8518 (tt0) cc_final: 0.8236 (tt0)
  outliers start: 2
  outliers final: 2
  residues processed: 87
  average time/residue: 0.4070
  time to fit residues: 37.4517
Evaluate side-chains
  82 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain B residue  222 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 81 optimal weight:   30.0000
   chunk 15 optimal weight:    0.9980
   chunk 41 optimal weight:    8.9990
   chunk 73 optimal weight:   20.0000
   chunk 45 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0270
   chunk 25 optimal weight:    5.9990
   chunk 64 optimal weight:    8.9990
   chunk 31 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
F  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.189986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.113851 restraints weight = 7163.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.48
r_work: 0.3058 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5858  Z= 0.128
  Angle     :  0.505   7.671   8040  Z= 0.247
  Chirality :  0.035   0.154   1002
  Planarity :  0.003   0.037   1022
  Dihedral  :  7.980  79.386    928
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 16.82 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.37), residues: 530
  helix:  1.84 (0.29), residues: 318
  sheet: -0.81 (0.53), residues: 90
  loop : -1.98 (0.49), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  68 
 TYR   0.010   0.001   TYR A 109 
 PHE   0.009   0.001   PHE B  56 
 TRP   0.015   0.002   TRP A 131 
 HIS   0.002   0.001   HIS A  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 5858)
  covalent geometry    : angle       0.50496 ( 8040)
  hydrogen bonds       : bond        0.02333 (  506)
  hydrogen bonds       : angle       3.48457 ( 1500)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A  128 TRP cc_start: 0.8341 (t60) cc_final: 0.8005 (t60)
REVERT: A  155 ASP cc_start: 0.8281 (m-30) cc_final: 0.7792 (m-30)
REVERT: A  198 LYS cc_start: 0.8521 (mtpt) cc_final: 0.8170 (mmmm)
REVERT: A  213 GLN cc_start: 0.8482 (tt0) cc_final: 0.8194 (tt0)
REVERT: B  128 TRP cc_start: 0.8356 (t60) cc_final: 0.7970 (t60)
REVERT: B  198 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8182 (mmmm)
REVERT: B  213 GLN cc_start: 0.8484 (tt0) cc_final: 0.8186 (tt0)
  outliers start: 6
  outliers final: 2
  residues processed: 88
  average time/residue: 0.3785
  time to fit residues: 35.2947
Evaluate side-chains
  78 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain B residue  222 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 30 optimal weight:    0.3980
   chunk 79 optimal weight:   20.0000
   chunk 0 optimal weight:    4.9990
   chunk 20 optimal weight:    0.5980
   chunk 53 optimal weight:   30.0000
   chunk 26 optimal weight:    0.7980
   chunk 76 optimal weight:   20.0000
   chunk 80 optimal weight:   20.0000
   chunk 23 optimal weight:    0.6980
   chunk 81 optimal weight:   30.0000
   overall best weight:    1.4982

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

Flipped N/Q/H residues before XYZ refinement:
F  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.187111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.110552 restraints weight = 7088.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 2.51
r_work: 0.2999 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   5858  Z= 0.227
  Angle     :  0.575   8.506   8040  Z= 0.284
  Chirality :  0.037   0.169   1002
  Planarity :  0.003   0.038   1022
  Dihedral  :  7.749  76.718    928
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 17.99 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.37), residues: 530
  helix:  1.63 (0.29), residues: 318
  sheet: -0.97 (0.52), residues: 90
  loop : -1.95 (0.50), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 126 
 TYR   0.011   0.002   TYR A 206 
 PHE   0.012   0.002   PHE B 146 
 TRP   0.021   0.002   TRP B 131 
 HIS   0.003   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 ( 5858)
  covalent geometry    : angle       0.57469 ( 8040)
  hydrogen bonds       : bond        0.02793 (  506)
  hydrogen bonds       : angle       3.70686 ( 1500)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  128 TRP cc_start: 0.8471 (t60) cc_final: 0.8093 (t60)
REVERT: A  155 ASP cc_start: 0.8421 (m-30) cc_final: 0.7962 (m-30)
REVERT: A  213 GLN cc_start: 0.8483 (tt0) cc_final: 0.8195 (tt0)
REVERT: B  128 TRP cc_start: 0.8484 (t60) cc_final: 0.8093 (t60)
REVERT: B  155 ASP cc_start: 0.8418 (m-30) cc_final: 0.7977 (m-30)
REVERT: B  213 GLN cc_start: 0.8498 (tt0) cc_final: 0.8207 (tt0)
  outliers start: 4
  outliers final: 2
  residues processed: 76
  average time/residue: 0.3646
  time to fit residues: 29.5081
Evaluate side-chains
  76 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain B residue  222 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 26 optimal weight:    0.1980
   chunk 33 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 40 optimal weight:    8.9990
   chunk 31 optimal weight:    0.5980
   chunk 58 optimal weight:   20.0000
   chunk 13 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 47 optimal weight:   20.0000
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.189534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.114810 restraints weight = 7138.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.50
r_work: 0.3060 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.3581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5858  Z= 0.115
  Angle     :  0.517   8.879   8040  Z= 0.252
  Chirality :  0.034   0.165   1002
  Planarity :  0.003   0.037   1022
  Dihedral  :  7.451  70.670    928
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 18.69 %
    Favored  : 79.91 %
  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 aren not related in a simple way.
  whole:  0.67 (0.37), residues: 530
  helix:  1.79 (0.29), residues: 318
  sheet: -0.97 (0.53), residues: 90
  loop : -2.01 (0.49), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 134 
 TYR   0.009   0.001   TYR B  91 
 PHE   0.009   0.001   PHE B  56 
 TRP   0.015   0.002   TRP A 131 
 HIS   0.002   0.001   HIS A 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 5858)
  covalent geometry    : angle       0.51709 ( 8040)
  hydrogen bonds       : bond        0.02284 (  506)
  hydrogen bonds       : angle       3.47931 ( 1500)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A  128 TRP cc_start: 0.8377 (t60) cc_final: 0.8035 (t60)
REVERT: A  155 ASP cc_start: 0.8326 (m-30) cc_final: 0.7851 (m-30)
REVERT: A  213 GLN cc_start: 0.8485 (tt0) cc_final: 0.8007 (tp40)
REVERT: B  128 TRP cc_start: 0.8375 (t60) cc_final: 0.7995 (t60)
REVERT: B  155 ASP cc_start: 0.8380 (m-30) cc_final: 0.7952 (m-30)
REVERT: B  213 GLN cc_start: 0.8496 (tt0) cc_final: 0.7934 (tp40)
  outliers start: 6
  outliers final: 6
  residues processed: 78
  average time/residue: 0.3763
  time to fit residues: 31.2337
Evaluate side-chains
  79 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain B residue   61 LYS
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  222 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 41 optimal weight:   20.0000
   chunk 47 optimal weight:   20.0000
   chunk 9 optimal weight:    0.5980
   chunk 51 optimal weight:   10.0000
   chunk 65 optimal weight:    0.0170
   chunk 19 optimal weight:    0.9980
   chunk 56 optimal weight:   20.0000
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 40 optimal weight:    5.9990
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 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 = 0.4269 r_free = 0.4269 target = 0.189633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.114155 restraints weight = 7098.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 2.46
r_work: 0.3069 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.3727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5858  Z= 0.116
  Angle     :  0.522   9.543   8040  Z= 0.252
  Chirality :  0.034   0.165   1002
  Planarity :  0.003   0.036   1022
  Dihedral  :  6.962  62.424    928
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 19.39 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.37), residues: 530
  helix:  1.96 (0.29), residues: 318
  sheet: -1.02 (0.53), residues: 90
  loop : -1.97 (0.49), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 134 
 TYR   0.008   0.001   TYR C  54 
 PHE   0.009   0.001   PHE B  56 
 TRP   0.023   0.002   TRP A 131 
 HIS   0.001   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 5858)
  covalent geometry    : angle       0.52158 ( 8040)
  hydrogen bonds       : bond        0.02256 (  506)
  hydrogen bonds       : angle       3.42617 ( 1500)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  128 TRP cc_start: 0.8378 (t60) cc_final: 0.8027 (t60)
REVERT: A  155 ASP cc_start: 0.8322 (m-30) cc_final: 0.7833 (m-30)
REVERT: A  213 GLN cc_start: 0.8513 (tt0) cc_final: 0.8226 (tt0)
REVERT: B  128 TRP cc_start: 0.8381 (t60) cc_final: 0.8042 (t60)
REVERT: B  155 ASP cc_start: 0.8366 (m-30) cc_final: 0.7931 (m-30)
REVERT: B  213 GLN cc_start: 0.8525 (tt0) cc_final: 0.7981 (tp40)
REVERT: F    8 LYS cc_start: 0.7747 (mttt) cc_final: 0.7079 (mtpp)
  outliers start: 6
  outliers final: 6
  residues processed: 77
  average time/residue: 0.3474
  time to fit residues: 28.4732
Evaluate side-chains
  78 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain B residue   61 LYS
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  222 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 70 optimal weight:   20.0000
   chunk 69 optimal weight:   20.0000
   chunk 25 optimal weight:    0.3980
   chunk 28 optimal weight:    0.6980
   chunk 80 optimal weight:   20.0000
   chunk 16 optimal weight:    0.9980
   chunk 48 optimal weight:   20.0000
   chunk 49 optimal weight:   10.0000
   chunk 67 optimal weight:    0.6980
   chunk 50 optimal weight:   20.0000
   chunk 65 optimal weight:    4.9990
   overall best weight:    1.5582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.187461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.109657 restraints weight = 7147.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.46
r_work: 0.2992 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work: 0.2831 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5858  Z= 0.225
  Angle     :  0.582  10.014   8040  Z= 0.282
  Chirality :  0.037   0.176   1002
  Planarity :  0.003   0.037   1022
  Dihedral  :  6.964  61.540    928
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 19.86 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.37), residues: 530
  helix:  1.71 (0.29), residues: 318
  sheet: -0.98 (0.53), residues: 90
  loop : -1.92 (0.51), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 126 
 TYR   0.013   0.002   TYR B 215 
 PHE   0.012   0.002   PHE A 146 
 TRP   0.035   0.002   TRP B 131 
 HIS   0.002   0.001   HIS A  78 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 5858)
  covalent geometry    : angle       0.58154 ( 8040)
  hydrogen bonds       : bond        0.02635 (  506)
  hydrogen bonds       : angle       3.58971 ( 1500)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A  128 TRP cc_start: 0.8643 (t60) cc_final: 0.8288 (t60)
REVERT: A  155 ASP cc_start: 0.8433 (m-30) cc_final: 0.7953 (m-30)
REVERT: A  213 GLN cc_start: 0.8654 (tt0) cc_final: 0.8427 (tt0)
REVERT: B  128 TRP cc_start: 0.8595 (t60) cc_final: 0.8203 (t60)
REVERT: B  155 ASP cc_start: 0.8437 (m-30) cc_final: 0.7978 (m-30)
REVERT: B  213 GLN cc_start: 0.8662 (tt0) cc_final: 0.8405 (tt0)
REVERT: F    8 LYS cc_start: 0.7651 (mttt) cc_final: 0.6984 (mtpp)
  outliers start: 6
  outliers final: 6
  residues processed: 76
  average time/residue: 0.3957
  time to fit residues: 31.9428
Evaluate side-chains
  80 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain B residue   61 LYS
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  222 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 72 optimal weight:   20.0000
   chunk 45 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   chunk 3 optimal weight:    0.2980
   chunk 60 optimal weight:    4.9990
   chunk 24 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 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 = 0.4264 r_free = 0.4264 target = 0.189091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.112964 restraints weight = 7136.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 2.48
r_work: 0.3047 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.3990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5858  Z= 0.126
  Angle     :  0.531  10.182   8040  Z= 0.257
  Chirality :  0.035   0.167   1002
  Planarity :  0.003   0.037   1022
  Dihedral  :  6.728  56.918    928
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 20.56 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.37), residues: 530
  helix:  1.91 (0.29), residues: 318
  sheet: -1.03 (0.53), residues: 90
  loop : -1.89 (0.51), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  68 
 TYR   0.008   0.001   TYR A 215 
 PHE   0.009   0.001   PHE B  56 
 TRP   0.033   0.002   TRP A 131 
 HIS   0.002   0.001   HIS B 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5858)
  covalent geometry    : angle       0.53060 ( 8040)
  hydrogen bonds       : bond        0.02320 (  506)
  hydrogen bonds       : angle       3.46917 ( 1500)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  128 TRP cc_start: 0.8435 (t60) cc_final: 0.8084 (t60)
REVERT: A  155 ASP cc_start: 0.8347 (m-30) cc_final: 0.7871 (m-30)
REVERT: A  213 GLN cc_start: 0.8494 (tt0) cc_final: 0.8017 (tp40)
REVERT: B  128 TRP cc_start: 0.8395 (t60) cc_final: 0.8006 (t60)
REVERT: B  155 ASP cc_start: 0.8388 (m-30) cc_final: 0.7954 (m-30)
REVERT: B  213 GLN cc_start: 0.8502 (tt0) cc_final: 0.8026 (tp40)
REVERT: C    8 LYS cc_start: 0.7703 (mttt) cc_final: 0.7055 (mtpp)
REVERT: F    8 LYS cc_start: 0.7655 (mttt) cc_final: 0.6991 (mtpp)
  outliers start: 6
  outliers final: 6
  residues processed: 74
  average time/residue: 0.4294
  time to fit residues: 33.6198
Evaluate side-chains
  78 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain B residue   61 LYS
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  222 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 55 optimal weight:   30.0000
   chunk 41 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   chunk 56 optimal weight:   20.0000
   chunk 38 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 6 optimal weight:    0.1980
   chunk 54 optimal weight:   20.0000
   chunk 47 optimal weight:   20.0000
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 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 = 0.4248 r_free = 0.4248 target = 0.187401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.110572 restraints weight = 6945.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.48
r_work: 0.3011 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.4156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   5858  Z= 0.191
  Angle     :  0.563   9.878   8040  Z= 0.274
  Chirality :  0.036   0.174   1002
  Planarity :  0.003   0.038   1022
  Dihedral  :  6.529  53.021    928
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 20.33 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.37), residues: 530
  helix:  1.85 (0.29), residues: 318
  sheet: -1.04 (0.53), residues: 90
  loop : -1.89 (0.51), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 126 
 TYR   0.012   0.001   TYR B 215 
 PHE   0.010   0.002   PHE B 146 
 TRP   0.037   0.002   TRP A 131 
 HIS   0.002   0.001   HIS B  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 5858)
  covalent geometry    : angle       0.56276 ( 8040)
  hydrogen bonds       : bond        0.02528 (  506)
  hydrogen bonds       : angle       3.55099 ( 1500)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2373.38 seconds
wall clock time: 41 minutes 6.86 seconds (2466.86 seconds total)