Starting phenix.real_space_refine
on Fri Dec 27 16:38:52 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8equ_28546/12_2024/8equ_28546_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8equ_28546/12_2024/8equ_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_28546/12_2024/8equ_28546.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8equ_28546/12_2024/8equ_28546.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8equ_28546/12_2024/8equ_28546_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8equ_28546/12_2024/8equ_28546_neut.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'TYR:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 51
    Chain: "E"
      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, D, G, H, F
  Time building chain proxies: 3.86, per 1000 atoms: 0.67
  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: 1.54
  Conformation dependent library (CDL) restraints added in 755.4 milliseconds
  

  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: 0.50
  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: 1.70

  Time building geometry restraints manager: 1.73 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: 0.00
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:             0.880
  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:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     16.830
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:11.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.660
-------------------------------------------------------------------------------
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= 0.260
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (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
 TRP   0.011   0.002   TRP A 193 
 HIS   0.004   0.001   HIS A 204 
 PHE   0.010   0.001   PHE B  56 
 TYR   0.028   0.002   TYR B 206 
 ARG   0.003   0.001   ARG B  68 

*********************** 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  : 0.522 
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: 0.9252
  time to fit residues: 96.9467
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  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:   20.0000
   chunk 62 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 64 optimal weight:    7.9990
   chunk 24 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 47 optimal weight:   20.0000
   chunk 74 optimal weight:   20.0000
   overall best weight:    2.7788

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.064   5858  Z= 0.595
  Angle     :  0.679   8.454   8040  Z= 0.341
  Chirality :  0.042   0.161   1002
  Planarity :  0.004   0.040   1022
  Dihedral  :  9.753  99.876    928
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 12.38 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.35), residues: 530
  helix:  1.08 (0.28), residues: 318
  sheet: -0.63 (0.50), residues: 90
  loop : -1.80 (0.51), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 149 
 HIS   0.005   0.002   HIS B  78 
 PHE   0.026   0.004   PHE A  43 
 TYR   0.029   0.003   TYR B 215 
 ARG   0.004   0.001   ARG A 126 

*********************** 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: 4
    poor density    : 84
  time to evaluate  : 0.569 
Fit side-chains
REVERT: A   61 LYS cc_start: 0.8573 (mttm) cc_final: 0.8131 (mtpt)
REVERT: A  128 TRP cc_start: 0.8142 (t60) cc_final: 0.7800 (t60)
REVERT: A  213 GLN cc_start: 0.7990 (tt0) cc_final: 0.7709 (tt0)
REVERT: B   61 LYS cc_start: 0.8538 (mttm) cc_final: 0.8119 (mtpt)
REVERT: B  128 TRP cc_start: 0.8125 (t60) cc_final: 0.7756 (t60)
REVERT: B  213 GLN cc_start: 0.7997 (tt0) cc_final: 0.7712 (tt0)
  outliers start: 4
  outliers final: 3
  residues processed: 86
  average time/residue: 1.0514
  time to fit residues: 95.6764
Evaluate side-chains
  79 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
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 41 optimal weight:    8.9990
   chunk 23 optimal weight:    0.6980
   chunk 61 optimal weight:    7.9990
   chunk 50 optimal weight:   20.0000
   chunk 20 optimal weight:    0.5980
   chunk 74 optimal weight:   20.0000
   chunk 80 optimal weight:   20.0000
   chunk 66 optimal weight:    0.6980
   chunk 73 optimal weight:    9.9990
   chunk 25 optimal weight:    0.6980
   chunk 59 optimal weight:   30.0000
   overall best weight:    2.1382

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.3234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   5858  Z= 0.460
  Angle     :  0.587   7.802   8040  Z= 0.296
  Chirality :  0.039   0.133   1002
  Planarity :  0.004   0.042   1022
  Dihedral  :  9.432  97.806    928
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 16.59 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.36), residues: 530
  helix:  1.23 (0.29), residues: 318
  sheet: -0.94 (0.50), residues: 90
  loop : -1.95 (0.48), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 149 
 HIS   0.005   0.001   HIS B  78 
 PHE   0.012   0.003   PHE B 146 
 TYR   0.013   0.002   TYR B 215 
 ARG   0.004   0.001   ARG B  68 

*********************** 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
  85 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.569 
Fit side-chains
REVERT: A  128 TRP cc_start: 0.8152 (t60) cc_final: 0.7801 (t60)
REVERT: A  155 ASP cc_start: 0.8143 (m-30) cc_final: 0.7640 (m-30)
REVERT: A  182 HIS cc_start: 0.7243 (m-70) cc_final: 0.7031 (m-70)
REVERT: A  213 GLN cc_start: 0.7954 (tt0) cc_final: 0.7665 (tt0)
REVERT: B  128 TRP cc_start: 0.8132 (t60) cc_final: 0.7765 (t60)
REVERT: B  155 ASP cc_start: 0.8226 (m-30) cc_final: 0.7895 (m-30)
REVERT: B  213 GLN cc_start: 0.7962 (tt0) cc_final: 0.7680 (tt0)
  outliers start: 6
  outliers final: 4
  residues processed: 83
  average time/residue: 0.9758
  time to fit residues: 85.5335
Evaluate side-chains
  77 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
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   68 ARG
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 73 optimal weight:   20.0000
   chunk 56 optimal weight:   20.0000
   chunk 38 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 50 optimal weight:   20.0000
   chunk 74 optimal weight:   20.0000
   chunk 79 optimal weight:   20.0000
   chunk 39 optimal weight:    5.9990
   chunk 70 optimal weight:   20.0000
   chunk 21 optimal weight:    3.9990
   overall best weight:    2.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  78 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.061   5858  Z= 0.575
  Angle     :  0.651   9.131   8040  Z= 0.325
  Chirality :  0.040   0.152   1002
  Planarity :  0.004   0.043   1022
  Dihedral  :  9.163  91.637    928
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.52 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.35), residues: 530
  helix:  0.97 (0.28), residues: 318
  sheet: -0.89 (0.51), residues: 90
  loop : -2.02 (0.47), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 149 
 HIS   0.004   0.001   HIS B  78 
 PHE   0.017   0.003   PHE A 146 
 TYR   0.014   0.002   TYR B 109 
 ARG   0.004   0.001   ARG B 126 

*********************** 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
  82 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.548 
Fit side-chains
REVERT: A  128 TRP cc_start: 0.8219 (t60) cc_final: 0.7870 (t60)
REVERT: A  182 HIS cc_start: 0.7297 (m-70) cc_final: 0.7061 (m90)
REVERT: A  213 GLN cc_start: 0.7960 (tt0) cc_final: 0.7636 (tt0)
REVERT: B  128 TRP cc_start: 0.8197 (t60) cc_final: 0.7873 (t60)
REVERT: B  155 ASP cc_start: 0.8264 (m-30) cc_final: 0.7942 (m-30)
REVERT: B  213 GLN cc_start: 0.7965 (tt0) cc_final: 0.7644 (tt0)
  outliers start: 8
  outliers final: 6
  residues processed: 80
  average time/residue: 1.0843
  time to fit residues: 91.2604
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  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ARG
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   68 ARG
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 66 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 1 optimal weight:    0.5980
   chunk 59 optimal weight:   30.0000
   chunk 32 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 54 optimal weight:   20.0000
   chunk 0 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 71 optimal weight:   10.0000
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B  57 GLN
B  78 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.3987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5858  Z= 0.243
  Angle     :  0.521   7.715   8040  Z= 0.260
  Chirality :  0.035   0.151   1002
  Planarity :  0.003   0.040   1022
  Dihedral  :  8.728  86.648    928
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 19.39 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.36), residues: 530
  helix:  1.58 (0.29), residues: 306
  sheet: -1.03 (0.51), residues: 90
  loop : -1.75 (0.46), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 149 
 HIS   0.003   0.001   HIS B 204 
 PHE   0.010   0.002   PHE B  56 
 TYR   0.010   0.001   TYR B  91 
 ARG   0.004   0.001   ARG A  68 

*********************** 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
  88 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.561 
Fit side-chains
REVERT: A  128 TRP cc_start: 0.8101 (t60) cc_final: 0.7753 (t60)
REVERT: A  155 ASP cc_start: 0.8109 (m-30) cc_final: 0.7609 (m-30)
REVERT: A  213 GLN cc_start: 0.7946 (tt0) cc_final: 0.7620 (tt0)
REVERT: B  128 TRP cc_start: 0.8124 (t60) cc_final: 0.7797 (t60)
REVERT: B  155 ASP cc_start: 0.8165 (m-30) cc_final: 0.7792 (m-30)
REVERT: B  213 GLN cc_start: 0.7948 (tt0) cc_final: 0.7626 (tt0)
  outliers start: 13
  outliers final: 7
  residues processed: 82
  average time/residue: 0.8467
  time to fit residues: 74.4068
Evaluate side-chains
  79 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain F residue   62 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 71 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 46 optimal weight:   30.0000
   chunk 19 optimal weight:    0.9980
   chunk 79 optimal weight:   20.0000
   chunk 65 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 41 optimal weight:   30.0000
   chunk 76 optimal weight:   20.0000
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  70 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.4149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5858  Z= 0.223
  Angle     :  0.514   8.173   8040  Z= 0.255
  Chirality :  0.035   0.161   1002
  Planarity :  0.003   0.038   1022
  Dihedral  :  8.068  79.221    928
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 19.63 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.36), residues: 530
  helix:  1.68 (0.29), residues: 318
  sheet: -1.02 (0.52), residues: 90
  loop : -2.03 (0.49), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 149 
 HIS   0.002   0.001   HIS B  93 
 PHE   0.010   0.002   PHE A  56 
 TYR   0.013   0.001   TYR A 154 
 ARG   0.005   0.001   ARG A  68 

*********************** 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
  91 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.664 
Fit side-chains
REVERT: A  128 TRP cc_start: 0.8063 (t60) cc_final: 0.7668 (t60)
REVERT: A  134 ARG cc_start: 0.7622 (mmm-85) cc_final: 0.7380 (mmm-85)
REVERT: A  213 GLN cc_start: 0.7961 (tt0) cc_final: 0.7616 (tt0)
REVERT: B  128 TRP cc_start: 0.8060 (t60) cc_final: 0.7708 (t60)
REVERT: B  134 ARG cc_start: 0.7652 (mmm-85) cc_final: 0.7426 (mmm-85)
REVERT: B  155 ASP cc_start: 0.8131 (m-30) cc_final: 0.7762 (m-30)
REVERT: B  213 GLN cc_start: 0.7962 (tt0) cc_final: 0.7617 (tt0)
REVERT: C    7 CYS cc_start: 0.8265 (t) cc_final: 0.7977 (t)
REVERT: F    8 LYS cc_start: 0.7709 (mttt) cc_final: 0.6994 (mtpp)
  outliers start: 13
  outliers final: 9
  residues processed: 84
  average time/residue: 0.8713
  time to fit residues: 78.0177
Evaluate side-chains
  82 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
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   43 PHE
Chi-restraints excluded: chain B residue  182 HIS
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain F residue   62 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 57 optimal weight:   20.0000
   chunk 44 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 79 optimal weight:   20.0000
   chunk 49 optimal weight:   10.0000
   chunk 48 optimal weight:   20.0000
   chunk 36 optimal weight:    2.9990
   chunk 31 optimal weight:    0.4980
   chunk 47 optimal weight:   20.0000
   overall best weight:    1.6784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.4302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   5858  Z= 0.379
  Angle     :  0.563   9.116   8040  Z= 0.279
  Chirality :  0.037   0.166   1002
  Planarity :  0.003   0.039   1022
  Dihedral  :  7.926  77.825    928
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 19.63 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.36), residues: 530
  helix:  1.60 (0.29), residues: 318
  sheet: -1.01 (0.52), residues: 90
  loop : -1.94 (0.49), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 131 
 HIS   0.004   0.001   HIS B  93 
 PHE   0.011   0.002   PHE B 146 
 TYR   0.015   0.002   TYR B 109 
 ARG   0.003   0.001   ARG A  68 

*********************** 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
  87 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.496 
Fit side-chains
REVERT: A  128 TRP cc_start: 0.8122 (t60) cc_final: 0.7740 (t60)
REVERT: A  155 ASP cc_start: 0.8142 (m-30) cc_final: 0.7700 (m-30)
REVERT: A  213 GLN cc_start: 0.7973 (tt0) cc_final: 0.7671 (tt0)
REVERT: B  128 TRP cc_start: 0.8138 (t60) cc_final: 0.7758 (t60)
REVERT: B  155 ASP cc_start: 0.8180 (m-30) cc_final: 0.7812 (m-30)
REVERT: B  213 GLN cc_start: 0.7980 (tt0) cc_final: 0.7677 (tt0)
REVERT: C    4 CYS cc_start: 0.8060 (m) cc_final: 0.7745 (t)
  outliers start: 15
  outliers final: 7
  residues processed: 82
  average time/residue: 0.8379
  time to fit residues: 73.2248
Evaluate side-chains
  79 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
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   43 PHE
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain C residue   74 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 50 optimal weight:   20.0000
   chunk 53 optimal weight:   30.0000
   chunk 39 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 62 optimal weight:    8.9990
   chunk 71 optimal weight:   10.0000
   chunk 75 optimal weight:   30.0000
   chunk 69 optimal weight:   20.0000
   chunk 73 optimal weight:   20.0000
   overall best weight:    2.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 116 GLN
B 116 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.4789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.064   5858  Z= 0.574
  Angle     :  0.657   9.621   8040  Z= 0.326
  Chirality :  0.040   0.170   1002
  Planarity :  0.004   0.040   1022
  Dihedral  :  7.944  76.252    928
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.86 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.36), residues: 530
  helix:  1.31 (0.29), residues: 318
  sheet: -0.97 (0.52), residues: 90
  loop : -1.85 (0.50), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 149 
 HIS   0.004   0.001   HIS B  78 
 PHE   0.016   0.003   PHE B 146 
 TYR   0.020   0.002   TYR B 154 
 ARG   0.004   0.001   ARG A 134 

*********************** 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
  86 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.452 
Fit side-chains
REVERT: A  128 TRP cc_start: 0.8220 (t60) cc_final: 0.7872 (t60)
REVERT: A  155 ASP cc_start: 0.8207 (m-30) cc_final: 0.7791 (m-30)
REVERT: A  213 GLN cc_start: 0.7997 (tt0) cc_final: 0.7696 (tt0)
REVERT: B  128 TRP cc_start: 0.8221 (t60) cc_final: 0.7870 (t60)
REVERT: B  155 ASP cc_start: 0.8215 (m-30) cc_final: 0.7828 (m-30)
REVERT: B  213 GLN cc_start: 0.8011 (tt0) cc_final: 0.7715 (tt0)
REVERT: C    4 CYS cc_start: 0.8126 (m) cc_final: 0.7820 (t)
REVERT: F    4 CYS cc_start: 0.8148 (m) cc_final: 0.7812 (t)
REVERT: F    7 CYS cc_start: 0.8295 (t) cc_final: 0.7963 (t)
  outliers start: 14
  outliers final: 9
  residues processed: 78
  average time/residue: 0.8525
  time to fit residues: 70.7771
Evaluate side-chains
  78 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  222 ASP
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  222 ASP
Chi-restraints excluded: chain C residue   74 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 75 optimal weight:   30.0000
   chunk 44 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 57 optimal weight:   20.0000
   chunk 22 optimal weight:    0.6980
   chunk 66 optimal weight:    0.0870
   chunk 69 optimal weight:   20.0000
   chunk 73 optimal weight:   20.0000
   chunk 48 optimal weight:   20.0000
   chunk 77 optimal weight:   30.0000
   chunk 47 optimal weight:   20.0000
   overall best weight:    4.4962

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.5357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.099   5858  Z= 0.914
  Angle     :  0.810  10.326   8040  Z= 0.403
  Chirality :  0.048   0.194   1002
  Planarity :  0.005   0.043   1022
  Dihedral  :  8.006  75.502    928
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 19.39 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.35), residues: 530
  helix:  0.88 (0.28), residues: 314
  sheet: -1.08 (0.50), residues: 90
  loop : -1.33 (0.54), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP A 149 
 HIS   0.007   0.002   HIS B  78 
 PHE   0.018   0.004   PHE B 146 
 TYR   0.023   0.003   TYR B 154 
 ARG   0.006   0.001   ARG B 126 

*********************** 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
  86 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.497 
Fit side-chains
REVERT: A  128 TRP cc_start: 0.8255 (t60) cc_final: 0.7959 (t60)
REVERT: A  155 ASP cc_start: 0.8244 (m-30) cc_final: 0.7857 (m-30)
REVERT: A  182 HIS cc_start: 0.7512 (m-70) cc_final: 0.7207 (m90)
REVERT: A  213 GLN cc_start: 0.8023 (tt0) cc_final: 0.7707 (tt0)
REVERT: B  128 TRP cc_start: 0.8246 (t60) cc_final: 0.7944 (t60)
REVERT: B  155 ASP cc_start: 0.8273 (m-30) cc_final: 0.7887 (m-30)
REVERT: B  213 GLN cc_start: 0.8019 (tt0) cc_final: 0.7711 (tt0)
REVERT: C    4 CYS cc_start: 0.8139 (m) cc_final: 0.7891 (t)
REVERT: F    4 CYS cc_start: 0.8174 (m) cc_final: 0.7874 (t)
REVERT: F    7 CYS cc_start: 0.8305 (t) cc_final: 0.7925 (t)
  outliers start: 16
  outliers final: 8
  residues processed: 77
  average time/residue: 0.9373
  time to fit residues: 76.7396
Evaluate side-chains
  77 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain C residue   74 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 54 optimal weight:   20.0000
   chunk 81 optimal weight:   20.0000
   chunk 75 optimal weight:   20.0000
   chunk 65 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 50 optimal weight:   20.0000
   chunk 39 optimal weight:    4.9990
   chunk 51 optimal weight:   10.0000
   chunk 69 optimal weight:   20.0000
   chunk 19 optimal weight:    0.6980
   overall best weight:    3.3388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.5422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.072   5858  Z= 0.693
  Angle     :  0.711  10.392   8040  Z= 0.353
  Chirality :  0.043   0.170   1002
  Planarity :  0.004   0.044   1022
  Dihedral  :  7.749  71.823    928
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.86 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.36), residues: 530
  helix:  1.04 (0.28), residues: 314
  sheet: -1.22 (0.47), residues: 98
  loop : -0.91 (0.58), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 149 
 HIS   0.006   0.002   HIS B  78 
 PHE   0.015   0.003   PHE A 105 
 TYR   0.018   0.002   TYR B 215 
 ARG   0.005   0.001   ARG B 126 

********************** 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
  81 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.540 
Fit side-chains
REVERT: A  128 TRP cc_start: 0.8238 (t60) cc_final: 0.7900 (t60)
REVERT: A  155 ASP cc_start: 0.8255 (m-30) cc_final: 0.7854 (m-30)
REVERT: A  213 GLN cc_start: 0.7991 (tt0) cc_final: 0.7693 (tt0)
REVERT: B  128 TRP cc_start: 0.8225 (t60) cc_final: 0.7877 (t60)
REVERT: B  155 ASP cc_start: 0.8243 (m-30) cc_final: 0.7862 (m-30)
REVERT: B  213 GLN cc_start: 0.7994 (tt0) cc_final: 0.7697 (tt0)
REVERT: C    4 CYS cc_start: 0.8123 (m) cc_final: 0.7831 (t)
REVERT: C    7 CYS cc_start: 0.8399 (t) cc_final: 0.8048 (t)
REVERT: F    4 CYS cc_start: 0.8149 (m) cc_final: 0.7849 (t)
REVERT: F    7 CYS cc_start: 0.8379 (t) cc_final: 0.8029 (t)
  outliers start: 12
  outliers final: 9
  residues processed: 79
  average time/residue: 1.1324
  time to fit residues: 94.0563
Evaluate side-chains
  77 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue   68 ARG
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain B residue   43 PHE
Chi-restraints excluded: chain B residue   61 LYS
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  197 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 59 optimal weight:   20.0000
   chunk 9 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 65 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 57 optimal weight:   20.0000
   chunk 3 optimal weight:    0.8980
   chunk 47 optimal weight:   20.0000
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4230 r_free = 0.4230 target = 0.186030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.109542 restraints weight = 7076.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 2.44
r_work: 0.3008 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work: 0.2847 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.5270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5858  Z= 0.245
  Angle     :  0.587  12.551   8040  Z= 0.284
  Chirality :  0.036   0.158   1002
  Planarity :  0.003   0.040   1022
  Dihedral  :  7.293  65.410    928
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 21.73 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.36), residues: 530
  helix:  1.65 (0.28), residues: 306
  sheet: -1.17 (0.51), residues: 94
  loop : -1.57 (0.50), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 149 
 HIS   0.003   0.001   HIS A 204 
 PHE   0.011   0.002   PHE A  56 
 TYR   0.016   0.001   TYR B 154 
 ARG   0.005   0.001   ARG A  68 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1984.90 seconds
wall clock time: 37 minutes 1.67 seconds (2221.67 seconds total)