Starting phenix.real_space_refine
on Fri Oct 10 11:30:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x7o_38105/10_2025/8x7o_38105.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x7o_38105/10_2025/8x7o_38105.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x7o_38105/10_2025/8x7o_38105.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x7o_38105/10_2025/8x7o_38105.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x7o_38105/10_2025/8x7o_38105.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x7o_38105/10_2025/8x7o_38105.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    2518      2.51       5
     N     704      2.21       5
     O     762      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3996
  Number of models: 1
  Model: ""
    Number of chains: 18
    Chain: "A"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 378
          Classifications: {'peptide': 55}
          Link IDs: {'CIS': 3, 'TRANS': 51}
    Chain: "B"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 378
          Classifications: {'peptide': 55}
          Link IDs: {'CIS': 3, 'TRANS': 51}
    Chain: "C"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 378
          Classifications: {'peptide': 55}
          Link IDs: {'CIS': 3, 'TRANS': 51}
    Chain: "D"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 378
          Classifications: {'peptide': 55}
          Link IDs: {'CIS': 3, 'TRANS': 51}
    Chain: "E"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 378
          Classifications: {'peptide': 55}
          Link IDs: {'CIS': 3, 'TRANS': 51}
    Chain: "F"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 378
          Classifications: {'peptide': 55}
          Link IDs: {'CIS': 3, 'TRANS': 51}
    Chain: "G"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 378
          Classifications: {'peptide': 55}
          Link IDs: {'CIS': 3, 'TRANS': 51}
    Chain: "H"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 378
          Classifications: {'peptide': 55}
          Link IDs: {'CIS': 3, 'TRANS': 51}
    Chain: "I"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 378
          Classifications: {'peptide': 55}
          Link IDs: {'CIS': 3, 'TRANS': 51}
    Chain: "J"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 378
          Classifications: {'peptide': 55}
          Link IDs: {'CIS': 3, 'TRANS': 51}
    Chain: "A"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 36
          Unusual residues: {'IZV': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 18
          Unusual residues: {'IZV': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 36
          Unusual residues: {'IZV': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 18
          Unusual residues: {'IZV': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 18
          Unusual residues: {'IZV': 1}
          Classifications: {'undetermined': 1}
    Chain: "G"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 36
          Unusual residues: {'IZV': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "I"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 18
          Unusual residues: {'IZV': 1}
          Classifications: {'undetermined': 1}
    Chain: "J"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 36
          Unusual residues: {'IZV': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.13, per 1000 atoms: 0.28
  Number of scatterers: 3996
  At special positions: 0
  Unit cell: (75.53, 110.39, 44.82, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      12     16.00
     O     762      8.00
     N     704      7.00
     C    2518      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: 0.40
  Conformation dependent library (CDL) restraints added in 161.3 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:  940

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 20.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 48
      removed outlier: 6.725A  pdb=" N   GLY A  47 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   GLY I  47 " --> pdb=" O   VAL J  48 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 64
      removed outlier: 6.422A  pdb=" N   VAL A  63 " --> pdb=" O   THR B  64 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   VAL I  63 " --> pdb=" O   THR J  64 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 71
      removed outlier: 6.511A  pdb=" N   VAL A  70 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   VAL I  70 " --> pdb=" O   VAL J  71 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 78
      removed outlier: 6.361A  pdb=" N   ALA A  76 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   THR E  75 " --> pdb=" O   ALA J  76 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   ALA J  78 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   VAL E  77 " --> pdb=" O   ALA J  78 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   ALA I  76 " --> pdb=" O   VAL J  77 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 93
      removed outlier: 8.873A  pdb=" N   ALA A  90 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 9.032A  pdb=" N   GLY B  93 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   THR A  92 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   ALA A  91 " --> pdb=" O   ALA E  90 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   THR E  92 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ALA E  91 " --> pdb=" O   ALA J  90 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   THR J  92 " --> pdb=" O   ALA E  91 " (cutoff:3.500A)
      removed outlier: 8.851A  pdb=" N   ALA I  90 " --> pdb=" O   ALA J  91 " (cutoff:3.500A)
      removed outlier: 9.012A  pdb=" N   GLY J  93 " --> pdb=" O   ALA I  90 " (cutoff:3.500A)
      removed outlier: 5.280A  pdb=" N   THR I  92 " --> pdb=" O   GLY J  93 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 46 through 48
      removed outlier: 6.723A  pdb=" N   GLY C  47 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   GLY F  47 " --> pdb=" O   VAL G  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 63 through 64
      removed outlier: 6.422A  pdb=" N   VAL C  63 " --> pdb=" O   THR D  64 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   VAL F  63 " --> pdb=" O   THR G  64 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 69 through 71
      removed outlier: 6.511A  pdb=" N   VAL C  70 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL F  70 " --> pdb=" O   VAL G  71 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 75 through 78
      removed outlier: 6.360A  pdb=" N   ALA C  76 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ALA F  76 " --> pdb=" O   VAL G  77 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 90 through 93
      removed outlier: 8.873A  pdb=" N   ALA C  90 " --> pdb=" O   ALA D  91 " (cutoff:3.500A)
      removed outlier: 9.032A  pdb=" N   GLY D  93 " --> pdb=" O   ALA C  90 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   THR C  92 " --> pdb=" O   GLY D  93 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   ALA C  91 " --> pdb=" O   ALA G  90 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   THR G  92 " --> pdb=" O   ALA C  91 " (cutoff:3.500A)
      removed outlier: 8.923A  pdb=" N   ALA F  90 " --> pdb=" O   ALA G  91 " (cutoff:3.500A)
      removed outlier: 9.084A  pdb=" N   GLY G  93 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   THR F  92 " --> pdb=" O   GLY G  93 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ALA F  91 " --> pdb=" O   ALA H  90 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   THR H  92 " --> pdb=" O   ALA F  91 " (cutoff:3.500A)

    33 hydrogen bonds defined for protein.
    99 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.66

  Time building geometry restraints manager: 0.54 seconds

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

  Histogram of bond lengths:
        1.21 -     1.30: 670
        1.30 -     1.38: 715
        1.38 -     1.47: 858
        1.47 -     1.56: 1759
        1.56 -     1.65: 28
  Bond restraints: 4030
  Sorted by residual:
  bond pdb=" C07 IZV J 202 "
       pdb=" S16 IZV J 202 "
    ideal  model  delta    sigma   weight residual
    1.766  1.607  0.159 2.00e-02 2.50e+03 6.31e+01
  bond pdb=" C07 IZV A 202 "
       pdb=" S16 IZV A 202 "
    ideal  model  delta    sigma   weight residual
    1.766  1.608  0.158 2.00e-02 2.50e+03 6.28e+01
  bond pdb=" C07 IZV I 201 "
       pdb=" S16 IZV I 201 "
    ideal  model  delta    sigma   weight residual
    1.766  1.608  0.158 2.00e-02 2.50e+03 6.28e+01
  bond pdb=" C07 IZV C 201 "
       pdb=" S16 IZV C 201 "
    ideal  model  delta    sigma   weight residual
    1.766  1.608  0.158 2.00e-02 2.50e+03 6.25e+01
  bond pdb=" C07 IZV E 201 "
       pdb=" S16 IZV E 201 "
    ideal  model  delta    sigma   weight residual
    1.766  1.608  0.158 2.00e-02 2.50e+03 6.25e+01
  ... (remaining 4025 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 4830
        2.31 -     4.62: 533
        4.62 -     6.93: 71
        6.93 -     9.24: 0
        9.24 -    11.55: 12
  Bond angle restraints: 5446
  Sorted by residual:
  angle pdb=" C07 IZV F 201 "
        pdb=" S16 IZV F 201 "
        pdb=" C17 IZV F 201 "
      ideal   model   delta    sigma   weight residual
      89.25  100.80  -11.55 3.00e+00 1.11e-01 1.48e+01
  angle pdb=" C07 IZV G 202 "
        pdb=" S16 IZV G 202 "
        pdb=" C17 IZV G 202 "
      ideal   model   delta    sigma   weight residual
      89.25  100.79  -11.54 3.00e+00 1.11e-01 1.48e+01
  angle pdb=" C07 IZV J 202 "
        pdb=" S16 IZV J 202 "
        pdb=" C17 IZV J 202 "
      ideal   model   delta    sigma   weight residual
      89.25  100.79  -11.54 3.00e+00 1.11e-01 1.48e+01
  angle pdb=" C07 IZV I 201 "
        pdb=" S16 IZV I 201 "
        pdb=" C17 IZV I 201 "
      ideal   model   delta    sigma   weight residual
      89.25  100.78  -11.53 3.00e+00 1.11e-01 1.48e+01
  angle pdb=" C07 IZV G 201 "
        pdb=" S16 IZV G 201 "
        pdb=" C17 IZV G 201 "
      ideal   model   delta    sigma   weight residual
      89.25  100.78  -11.53 3.00e+00 1.11e-01 1.48e+01
  ... (remaining 5441 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.34: 1825
       10.34 -    20.68: 335
       20.68 -    31.02: 60
       31.02 -    41.36: 0
       41.36 -    51.69: 20
  Dihedral angle restraints: 2240
    sinusoidal: 760
      harmonic: 1480
  Sorted by residual:
  dihedral pdb=" CA  GLY D  67 "
           pdb=" C   GLY D  67 "
           pdb=" N   GLY D  68 "
           pdb=" CA  GLY D  68 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   25.07  -25.07     0      5.00e+00 4.00e-02 2.51e+01
  dihedral pdb=" CA  GLY F  67 "
           pdb=" C   GLY F  67 "
           pdb=" N   GLY F  68 "
           pdb=" CA  GLY F  68 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   25.04  -25.04     0      5.00e+00 4.00e-02 2.51e+01
  dihedral pdb=" CA  GLY I  67 "
           pdb=" C   GLY I  67 "
           pdb=" N   GLY I  68 "
           pdb=" CA  GLY I  68 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   25.02  -25.02     0      5.00e+00 4.00e-02 2.50e+01
  ... (remaining 2237 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 365
       0.052 -    0.104: 169
       0.104 -    0.156: 96
       0.156 -    0.208: 20
       0.208 -    0.260: 20
  Chirality restraints: 670
  Sorted by residual:
  chirality pdb=" CA  ILE E  88 "
            pdb=" N   ILE E  88 "
            pdb=" C   ILE E  88 "
            pdb=" CB  ILE E  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CA  ILE J  88 "
            pdb=" N   ILE J  88 "
            pdb=" C   ILE J  88 "
            pdb=" CB  ILE J  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CA  ILE B  88 "
            pdb=" N   ILE B  88 "
            pdb=" C   ILE B  88 "
            pdb=" CB  ILE B  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.26 2.00e-01 2.50e+01 1.64e+00
  ... (remaining 667 not shown)

  Planarity restraints: 664
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  52 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.14e+00
        pdb=" C   VAL B  52 "    0.039 2.00e-02 2.50e+03
        pdb=" O   VAL B  52 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ALA B  53 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL H  52 "    0.011 2.00e-02 2.50e+03   2.26e-02 5.11e+00
        pdb=" C   VAL H  52 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   VAL H  52 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ALA H  53 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D  52 "    0.011 2.00e-02 2.50e+03   2.26e-02 5.11e+00
        pdb=" C   VAL D  52 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   VAL D  52 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ALA D  53 "    0.013 2.00e-02 2.50e+03
  ... (remaining 661 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 971
        2.80 -     3.33: 3192
        3.33 -     3.85: 6252
        3.85 -     4.38: 7329
        4.38 -     4.90: 14297
  Nonbonded interactions: 32041
  Sorted by model distance:
  nonbonded pdb=" CE1 HIS C  50 "
            pdb=" O01 IZV C 201 "
     model   vdw
     2.280 3.260
  nonbonded pdb=" CE1 HIS A  50 "
            pdb=" O01 IZV A 201 "
     model   vdw
     2.315 3.260
  nonbonded pdb=" CE1 HIS E  50 "
            pdb=" O01 IZV E 201 "
     model   vdw
     2.363 3.260
  nonbonded pdb=" CE1 HIS G  50 "
            pdb=" O01 IZV G 201 "
     model   vdw
     2.417 3.260
  nonbonded pdb=" OG1 THR F  64 "
            pdb=" OG1 THR H  54 "
     model   vdw
     2.514 3.040
  ... (remaining 32036 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'I'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.860
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     6.510
  Find NCS groups from input model:        0.040
  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:2.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5694
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      :  0.019   0.159   4030  Z= 0.951
  Angle     :  1.484  11.548   5446  Z= 0.791
  Chirality :  0.081   0.260    670
  Planarity :  0.006   0.023    664
  Dihedral  : 11.598  51.694   1300
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 17.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.79 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 5.56 %
    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: -4.07 (0.28), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.016   0.008   PHE C  94 
 HIS   0.002   0.001   HIS G  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.01942 ( 4030)
  covalent geometry    : angle       1.48420 ( 5446)
  hydrogen bonds       : bond        0.19147 (   33)
  hydrogen bonds       : angle       8.64563 (   99)

*********************** 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
  93 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
REVERT: B   80 LYS cc_start: 0.7941 (tppp) cc_final: 0.6263 (pttm)
REVERT: B   83 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8134 (mt-10)
REVERT: D   83 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8219 (mt-10)
REVERT: E   98 ASP cc_start: 0.6421 (m-30) cc_final: 0.5262 (m-30)
REVERT: F   98 ASP cc_start: 0.6278 (m-30) cc_final: 0.5816 (m-30)
REVERT: G   98 ASP cc_start: 0.6963 (m-30) cc_final: 0.6533 (m-30)
REVERT: I   96 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7698 (tttt)
REVERT: J   96 LYS cc_start: 0.7185 (mtpt) cc_final: 0.6971 (tttp)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1099
  time to fit residues: 11.8359
Evaluate side-chains
  74 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.162302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.120446 restraints weight = 4466.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.124875 restraints weight = 2195.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.127512 restraints weight = 1472.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.129274 restraints weight = 1175.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.130197 restraints weight = 1029.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.4148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4030  Z= 0.118
  Angle     :  0.559   4.058   5446  Z= 0.303
  Chirality :  0.052   0.152    670
  Planarity :  0.002   0.013    664
  Dihedral  :  5.462  16.480    540
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 18.68 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 5.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.54 (0.31), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.23), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.003   PHE E  94 
 HIS   0.004   0.001   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 4030)
  covalent geometry    : angle       0.55861 ( 5446)
  hydrogen bonds       : bond        0.01356 (   33)
  hydrogen bonds       : angle       5.60923 (   99)

*********************** 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
  92 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7879 (mt-10)
REVERT: B   79 GLN cc_start: 0.9077 (tt0) cc_final: 0.8857 (mt0)
REVERT: D   46 LYS cc_start: 0.7342 (tttt) cc_final: 0.6583 (mmmt)
REVERT: H   96 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8220 (tttt)
REVERT: I   96 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8162 (tttt)
REVERT: J   65 ASN cc_start: 0.8607 (t0) cc_final: 0.8352 (t0)
  outliers start: 12
  outliers final: 1
  residues processed: 83
  average time/residue: 0.0938
  time to fit residues: 9.2746
Evaluate side-chains
  68 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   96 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 30 optimal weight:   20.0000
   chunk 39 optimal weight:   20.0000
   chunk 44 optimal weight:   20.0000
   chunk 18 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 15 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 29 optimal weight:    8.9990
   overall best weight:    7.5990

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

Flipped N/Q/H residues before XYZ refinement:
** E  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.136629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.092245 restraints weight = 4502.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.095392 restraints weight = 2443.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.097516 restraints weight = 1788.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.098531 restraints weight = 1507.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.099239 restraints weight = 1375.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.7509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.047   4030  Z= 0.407
  Angle     :  0.773   5.168   5446  Z= 0.417
  Chirality :  0.059   0.166    670
  Planarity :  0.003   0.013    664
  Dihedral  :  6.433  17.854    540
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 15.53 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 5.56 %
    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: -4.31 (0.26), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.28 (0.20), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.003   PHE D  94 
 HIS   0.002   0.001   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00917 ( 4030)
  covalent geometry    : angle       0.77330 ( 5446)
  hydrogen bonds       : bond        0.02654 (   33)
  hydrogen bonds       : angle       5.94890 (   99)

*********************** 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
  111 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.170 
Fit side-chains
REVERT: C   46 LYS cc_start: 0.8253 (tttt) cc_final: 0.7864 (mptt)
REVERT: D   46 LYS cc_start: 0.8431 (tttt) cc_final: 0.7661 (tppt)
REVERT: D   96 LYS cc_start: 0.8778 (tttm) cc_final: 0.8323 (tttp)
REVERT: D   97 LYS cc_start: 0.8962 (mmtt) cc_final: 0.7878 (mmtt)
REVERT: D   98 ASP cc_start: 0.8383 (m-30) cc_final: 0.7709 (m-30)
REVERT: F   57 GLU cc_start: 0.8249 (mp0) cc_final: 0.7832 (mp0)
REVERT: G   87 SER cc_start: 0.8898 (p) cc_final: 0.8688 (p)
  outliers start: 24
  outliers final: 9
  residues processed: 106
  average time/residue: 0.0919
  time to fit residues: 11.5892
Evaluate side-chains
  89 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain I residue   49 VAL
Chi-restraints excluded: chain J residue   49 VAL
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   60 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    6.9990
   chunk 39 optimal weight:    0.0470
   chunk 11 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 9 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   overall best weight:    2.2084

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

Flipped N/Q/H residues before XYZ refinement:
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.136925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.092876 restraints weight = 4474.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.095858 restraints weight = 2598.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.097929 restraints weight = 1935.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.098780 restraints weight = 1628.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.099698 restraints weight = 1501.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.7668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4030  Z= 0.130
  Angle     :  0.538   4.056   5446  Z= 0.289
  Chirality :  0.052   0.155    670
  Planarity :  0.002   0.013    664
  Dihedral  :  5.309  15.684    540
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 13.42 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 5.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.83 (0.29), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.91 (0.22), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.002   PHE E  94 
 HIS   0.001   0.000   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4030)
  covalent geometry    : angle       0.53772 ( 5446)
  hydrogen bonds       : bond        0.01407 (   33)
  hydrogen bonds       : angle       4.76035 (   99)

*********************** 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
  98 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.156 
Fit side-chains
REVERT: B   46 LYS cc_start: 0.8617 (tttt) cc_final: 0.7748 (tppt)
REVERT: B   97 LYS cc_start: 0.9004 (mmtt) cc_final: 0.7872 (mmtt)
REVERT: C   46 LYS cc_start: 0.8273 (tttt) cc_final: 0.7988 (mptt)
REVERT: D   46 LYS cc_start: 0.8585 (tttt) cc_final: 0.7824 (tppt)
REVERT: D   83 GLU cc_start: 0.8317 (mp0) cc_final: 0.7823 (mp0)
REVERT: G   46 LYS cc_start: 0.7883 (mptt) cc_final: 0.7681 (tptt)
REVERT: J   46 LYS cc_start: 0.8461 (tttm) cc_final: 0.8052 (tptt)
REVERT: J   79 GLN cc_start: 0.9447 (OUTLIER) cc_final: 0.9214 (mt0)
REVERT: J   96 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.7900 (mtpp)
  outliers start: 21
  outliers final: 12
  residues processed: 95
  average time/residue: 0.0996
  time to fit residues: 11.0685
Evaluate side-chains
  91 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain E residue   52 VAL
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   96 LYS
Chi-restraints excluded: chain I residue   96 LYS
Chi-restraints excluded: chain J residue   79 GLN
Chi-restraints excluded: chain J residue   96 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 44 optimal weight:   20.0000
   chunk 4 optimal weight:   20.0000
   chunk 36 optimal weight:    9.9990
   chunk 37 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 41 optimal weight:    0.0870
   chunk 38 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 29 optimal weight:   20.0000
   overall best weight:    4.6166

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

Flipped N/Q/H residues before XYZ refinement:
C  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.133863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.088650 restraints weight = 4503.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.091664 restraints weight = 2592.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.093633 restraints weight = 1929.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.094916 restraints weight = 1634.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.095751 restraints weight = 1476.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.8030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   4030  Z= 0.241
  Angle     :  0.619   4.376   5446  Z= 0.330
  Chirality :  0.054   0.157    670
  Planarity :  0.002   0.016    664
  Dihedral  :  5.656  16.924    540
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 12.89 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 5.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.90 (0.29), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.97 (0.22), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.002   PHE A  94 
 HIS   0.003   0.001   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00545 ( 4030)
  covalent geometry    : angle       0.61884 ( 5446)
  hydrogen bonds       : bond        0.01804 (   33)
  hydrogen bonds       : angle       5.24954 (   99)

*********************** 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
  108 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.174 
Fit side-chains
REVERT: B   46 LYS cc_start: 0.8562 (tttt) cc_final: 0.7606 (tppt)
REVERT: B   79 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8971 (mt0)
REVERT: B   97 LYS cc_start: 0.8945 (mmtt) cc_final: 0.7832 (mmtt)
REVERT: C   46 LYS cc_start: 0.8362 (tttt) cc_final: 0.7945 (mptt)
REVERT: D   46 LYS cc_start: 0.8516 (tttt) cc_final: 0.7755 (tppt)
REVERT: G   46 LYS cc_start: 0.8034 (mptt) cc_final: 0.7782 (tptt)
REVERT: J   46 LYS cc_start: 0.8598 (tttm) cc_final: 0.8304 (tptt)
REVERT: J   96 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8232 (mtpt)
  outliers start: 24
  outliers final: 20
  residues processed: 100
  average time/residue: 0.0982
  time to fit residues: 11.5805
Evaluate side-chains
  107 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   79 GLN
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain E residue   52 VAL
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   96 LYS
Chi-restraints excluded: chain I residue   49 VAL
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain I residue   96 LYS
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   96 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 10 optimal weight:   20.0000
   chunk 16 optimal weight:    9.9990
   chunk 7 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   chunk 35 optimal weight:    9.9990
   chunk 17 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 2 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    4.3988

-------------------------------------------------------------------------------
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 = 0.4155 r_free = 0.4155 target = 0.134733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.089898 restraints weight = 4652.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.093134 restraints weight = 2558.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.095323 restraints weight = 1861.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.096580 restraints weight = 1552.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.097166 restraints weight = 1400.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.8350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   4030  Z= 0.230
  Angle     :  0.603   4.410   5446  Z= 0.322
  Chirality :  0.054   0.156    670
  Planarity :  0.002   0.012    664
  Dihedral  :  5.490  17.168    540
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  7.63 %
    Allowed  : 12.11 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 5.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.83 (0.30), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.91 (0.23), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.002   PHE D  94 
 HIS   0.002   0.001   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 4030)
  covalent geometry    : angle       0.60332 ( 5446)
  hydrogen bonds       : bond        0.01717 (   33)
  hydrogen bonds       : angle       4.99638 (   99)

*********************** 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
  113 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 84
  time to evaluate  : 0.143 
Fit side-chains
REVERT: B   46 LYS cc_start: 0.8591 (tttt) cc_final: 0.7553 (tppt)
REVERT: B   97 LYS cc_start: 0.8881 (mmtt) cc_final: 0.7773 (mmtt)
REVERT: C   46 LYS cc_start: 0.8384 (tttt) cc_final: 0.7922 (mptt)
REVERT: D   46 LYS cc_start: 0.8570 (tttt) cc_final: 0.7713 (tppt)
REVERT: D   83 GLU cc_start: 0.8502 (mp0) cc_final: 0.7965 (mp0)
REVERT: G   46 LYS cc_start: 0.8203 (mptt) cc_final: 0.7907 (tptt)
REVERT: J   96 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8176 (mtpt)
  outliers start: 29
  outliers final: 24
  residues processed: 104
  average time/residue: 0.0957
  time to fit residues: 11.7552
Evaluate side-chains
  108 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain E residue   52 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain H residue   96 LYS
Chi-restraints excluded: chain I residue   49 VAL
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain I residue   96 LYS
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   96 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 32 optimal weight:    8.9990
   chunk 20 optimal weight:   20.0000
   chunk 5 optimal weight:   20.0000
   chunk 39 optimal weight:    9.9990
   chunk 8 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   chunk 17 optimal weight:    0.4980
   chunk 26 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    5.8988

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

Flipped N/Q/H residues before XYZ refinement:
C  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.132398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.087053 restraints weight = 4701.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.090424 restraints weight = 2641.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.092482 restraints weight = 1933.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.093854 restraints weight = 1627.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.094266 restraints weight = 1466.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.8604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.034   4030  Z= 0.303
  Angle     :  0.666   4.802   5446  Z= 0.355
  Chirality :  0.057   0.161    670
  Planarity :  0.002   0.010    664
  Dihedral  :  5.759  18.247    540
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.25 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  7.89 %
    Allowed  : 12.37 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 5.56 %
    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: -4.06 (0.30), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.09 (0.23), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.009   0.002   PHE D  94 
 HIS   0.002   0.001   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00681 ( 4030)
  covalent geometry    : angle       0.66618 ( 5446)
  hydrogen bonds       : bond        0.01989 (   33)
  hydrogen bonds       : angle       5.33581 (   99)

*********************** 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
  119 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 89
  time to evaluate  : 0.160 
Fit side-chains
REVERT: B   46 LYS cc_start: 0.8614 (tttt) cc_final: 0.7643 (tppt)
REVERT: B   97 LYS cc_start: 0.8883 (mmtt) cc_final: 0.7793 (mmtt)
REVERT: C   46 LYS cc_start: 0.8411 (tttt) cc_final: 0.7918 (mptt)
REVERT: D   46 LYS cc_start: 0.8572 (tttt) cc_final: 0.7655 (tppt)
REVERT: D   83 GLU cc_start: 0.8577 (mp0) cc_final: 0.8076 (mp0)
REVERT: G   46 LYS cc_start: 0.8234 (mptt) cc_final: 0.7937 (tptt)
REVERT: J   46 LYS cc_start: 0.8440 (tttm) cc_final: 0.8157 (tttp)
REVERT: J   96 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8287 (tttm)
  outliers start: 30
  outliers final: 29
  residues processed: 110
  average time/residue: 0.0973
  time to fit residues: 12.6014
Evaluate side-chains
  117 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 87
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain E residue   52 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain H residue   96 LYS
Chi-restraints excluded: chain I residue   49 VAL
Chi-restraints excluded: chain I residue   52 VAL
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain I residue   96 LYS
Chi-restraints excluded: chain J residue   49 VAL
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   87 SER
Chi-restraints excluded: chain J residue   96 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 24 optimal weight:    0.2980
   chunk 46 optimal weight:    5.9990
   chunk 25 optimal weight:   20.0000
   chunk 27 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    3.0588

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

Flipped N/Q/H residues before XYZ refinement:
C  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.141379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.095845 restraints weight = 4475.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.099538 restraints weight = 2317.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.101840 restraints weight = 1651.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.103150 restraints weight = 1376.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.103443 restraints weight = 1248.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.8684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4030  Z= 0.171
  Angle     :  0.600   6.160   5446  Z= 0.317
  Chirality :  0.053   0.154    670
  Planarity :  0.002   0.015    664
  Dihedral  :  5.200  16.993    540
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  7.11 %
    Allowed  : 13.68 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 5.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.88 (0.31), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.95 (0.23), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.001   PHE E  94 
 HIS   0.001   0.000   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 4030)
  covalent geometry    : angle       0.59993 ( 5446)
  hydrogen bonds       : bond        0.01358 (   33)
  hydrogen bonds       : angle       4.67461 (   99)

*********************** 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
  113 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 86
  time to evaluate  : 0.171 
Fit side-chains
REVERT: B   46 LYS cc_start: 0.8611 (tttt) cc_final: 0.7654 (tppt)
REVERT: B   97 LYS cc_start: 0.8840 (mttt) cc_final: 0.7755 (mmtt)
REVERT: C   46 LYS cc_start: 0.8346 (tttt) cc_final: 0.7873 (mptt)
REVERT: D   46 LYS cc_start: 0.8553 (tttt) cc_final: 0.7656 (tppt)
REVERT: D   83 GLU cc_start: 0.8470 (mp0) cc_final: 0.7897 (mp0)
REVERT: G   46 LYS cc_start: 0.8304 (mptt) cc_final: 0.7960 (tptt)
REVERT: J   96 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8145 (mtpt)
  outliers start: 27
  outliers final: 23
  residues processed: 105
  average time/residue: 0.1081
  time to fit residues: 13.2455
Evaluate side-chains
  111 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain E residue   52 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain H residue   96 LYS
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain I residue   96 LYS
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   96 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 43 optimal weight:    2.9990
   chunk 13 optimal weight:    8.9990
   chunk 30 optimal weight:   20.0000
   chunk 19 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 15 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 46 optimal weight:    9.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
C  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.137395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.091493 restraints weight = 4643.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.094995 restraints weight = 2433.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.097327 restraints weight = 1756.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.098599 restraints weight = 1462.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.099132 restraints weight = 1322.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.8836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.041   4030  Z= 0.360
  Angle     :  0.731   5.597   5446  Z= 0.389
  Chirality :  0.059   0.163    670
  Planarity :  0.002   0.007    664
  Dihedral  :  5.811  18.539    540
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.34 %
    Favored  : 85.66 %
  Rotamer:
    Outliers :  7.89 %
    Allowed  : 13.68 %
    Favored  : 78.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 5.56 %
    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: -4.19 (0.30), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.23), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.011   0.002   PHE A  94 
 HIS   0.002   0.001   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00811 ( 4030)
  covalent geometry    : angle       0.73148 ( 5446)
  hydrogen bonds       : bond        0.02208 (   33)
  hydrogen bonds       : angle       5.39505 (   99)

*********************** 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
  120 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 90
  time to evaluate  : 0.088 
Fit side-chains
REVERT: B   46 LYS cc_start: 0.8675 (tttt) cc_final: 0.7736 (tppt)
REVERT: B   61 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8335 (mt-10)
REVERT: B   97 LYS cc_start: 0.8911 (mttt) cc_final: 0.7832 (mmtt)
REVERT: C   46 LYS cc_start: 0.8461 (tttt) cc_final: 0.7956 (mptt)
REVERT: D   46 LYS cc_start: 0.8600 (tttt) cc_final: 0.7647 (tppt)
REVERT: D   83 GLU cc_start: 0.8588 (mp0) cc_final: 0.8110 (mp0)
REVERT: E   98 ASP cc_start: 0.8725 (m-30) cc_final: 0.8458 (m-30)
REVERT: J   46 LYS cc_start: 0.8260 (tttm) cc_final: 0.7922 (tttp)
REVERT: J   96 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8260 (mtpt)
  outliers start: 30
  outliers final: 28
  residues processed: 109
  average time/residue: 0.0952
  time to fit residues: 12.1450
Evaluate side-chains
  120 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 91
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain E residue   52 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain H residue   96 LYS
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain I residue   96 LYS
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   87 SER
Chi-restraints excluded: chain J residue   96 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 10 optimal weight:   20.0000
   chunk 12 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 23 optimal weight:    8.9990
   chunk 25 optimal weight:   20.0000
   chunk 19 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 40 optimal weight:   20.0000
   chunk 29 optimal weight:    8.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
C  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.137907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.091854 restraints weight = 4548.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.095455 restraints weight = 2403.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.097635 restraints weight = 1737.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.098702 restraints weight = 1461.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.099563 restraints weight = 1340.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.8995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.043   4030  Z= 0.347
  Angle     :  0.743   5.850   5446  Z= 0.395
  Chirality :  0.058   0.162    670
  Planarity :  0.002   0.012    664
  Dihedral  :  5.825  19.215    540
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.89 %
    Favored  : 88.11 %
  Rotamer:
    Outliers :  7.63 %
    Allowed  : 13.42 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 5.56 %
    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: -4.29 (0.30), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.26 (0.23), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.010   0.002   PHE E  94 
 HIS   0.001   0.001   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00782 ( 4030)
  covalent geometry    : angle       0.74321 ( 5446)
  hydrogen bonds       : bond        0.02223 (   33)
  hydrogen bonds       : angle       5.37899 (   99)

********************** 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
  120 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 91
  time to evaluate  : 0.138 
Fit side-chains
REVERT: B   46 LYS cc_start: 0.8634 (tttt) cc_final: 0.7692 (tppt)
REVERT: B   61 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8373 (mt-10)
REVERT: B   97 LYS cc_start: 0.8902 (mttt) cc_final: 0.7830 (mmtt)
REVERT: C   46 LYS cc_start: 0.8417 (tttt) cc_final: 0.7903 (mptt)
REVERT: D   46 LYS cc_start: 0.8597 (tttt) cc_final: 0.7609 (tppt)
REVERT: D   83 GLU cc_start: 0.8590 (mp0) cc_final: 0.8072 (mp0)
REVERT: E   98 ASP cc_start: 0.8688 (m-30) cc_final: 0.8474 (m-30)
REVERT: G   46 LYS cc_start: 0.8335 (mmtm) cc_final: 0.7977 (tptt)
REVERT: J   46 LYS cc_start: 0.8274 (tttm) cc_final: 0.7969 (tttp)
REVERT: J   96 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8280 (mtpt)
  outliers start: 29
  outliers final: 27
  residues processed: 110
  average time/residue: 0.1014
  time to fit residues: 13.0450
Evaluate side-chains
  119 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 91
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   57 GLU
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   52 VAL
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   87 SER
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   87 SER
Chi-restraints excluded: chain H residue   96 LYS
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain I residue   96 LYS
Chi-restraints excluded: chain J residue   52 VAL
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   87 SER
Chi-restraints excluded: chain J residue   96 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 8 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
C  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.143043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.097037 restraints weight = 4453.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.100806 restraints weight = 2302.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.103037 restraints weight = 1642.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.104400 restraints weight = 1376.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.105163 restraints weight = 1249.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.9059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4030  Z= 0.136
  Angle     :  0.608   5.887   5446  Z= 0.320
  Chirality :  0.053   0.149    670
  Planarity :  0.001   0.009    664
  Dihedral  :  5.065  16.472    540
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 16.58 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 5.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.96 (0.31), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (0.24), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.005   0.001   PHE E  94 
 HIS   0.001   0.000   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 4030)
  covalent geometry    : angle       0.60819 ( 5446)
  hydrogen bonds       : bond        0.01214 (   33)
  hydrogen bonds       : angle       4.46106 (   99)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 831.60 seconds
wall clock time: 15 minutes 12.13 seconds (912.13 seconds total)