Starting phenix.real_space_refine
on Wed Mar  5 22:42:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x7o_38105/03_2025/8x7o_38105.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x7o_38105/03_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_38105/03_2025/8x7o_38105.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x7o_38105/03_2025/8x7o_38105.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x7o_38105/03_2025/8x7o_38105.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x7o_38105/03_2025/8x7o_38105.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.91, per 1000 atoms: 0.73
  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: 1.10
  Conformation dependent library (CDL) restraints added in 567.5 milliseconds
  

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  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: 0.86
  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: 0.89

  Time building geometry restraints manager: 1.30 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'J'
}

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:             1.260
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.320
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.060
-------------------------------------------------------------------------------
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= 1.144
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 HIS   0.002   0.001   HIS G  50 
 PHE   0.016   0.008   PHE C  94 

*********************** 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  : 0.482 
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: 0.2346
  time to fit residues: 25.5544
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  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 37 optimal weight:    0.7980
   chunk 21 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    3.3588

-------------------------------------------------------------------------------
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**
H  62 GLN
I  62 GLN
** J  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.155222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.109457 restraints weight = 4219.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.113720 restraints weight = 2113.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.116333 restraints weight = 1459.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.5642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4030  Z= 0.298
  Angle     :  0.664   4.733   5446  Z= 0.352
  Chirality :  0.055   0.167    670
  Planarity :  0.003   0.015    664
  Dihedral  :  5.927  18.491    540
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 17.89 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 5.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.75 (0.29), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.85 (0.22), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS D  50 
 PHE   0.021   0.004   PHE E  94 

*********************** 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
  94 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.414 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8104 (tttt) cc_final: 0.7376 (tppt)
REVERT: H   96 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8238 (tttm)
REVERT: I   79 GLN cc_start: 0.9330 (tt0) cc_final: 0.9093 (tt0)
  outliers start: 16
  outliers final: 5
  residues processed: 86
  average time/residue: 0.1936
  time to fit residues: 20.1273
Evaluate side-chains
  72 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   49 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 18 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 31 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 11 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 42 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    4.1990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.137548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.093630 restraints weight = 4408.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.096772 restraints weight = 2434.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.098804 restraints weight = 1785.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.7295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4030  Z= 0.368
  Angle     :  0.623   4.868   5446  Z= 0.336
  Chirality :  0.054   0.164    670
  Planarity :  0.002   0.010    664
  Dihedral  :  5.866  16.367    540
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  7.11 %
    Allowed  : 13.16 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.96 (0.27), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (0.21), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G  50 
 PHE   0.012   0.002   PHE C  94 

*********************** 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
  103 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 76
  time to evaluate  : 0.434 
Fit side-chains
REVERT: B   46 LYS cc_start: 0.8551 (tttt) cc_final: 0.7706 (tppt)
REVERT: B   96 LYS cc_start: 0.8568 (tttm) cc_final: 0.8289 (tttp)
REVERT: B   97 LYS cc_start: 0.8936 (mttt) cc_final: 0.7928 (mmtt)
REVERT: D   46 LYS cc_start: 0.8559 (tttt) cc_final: 0.7774 (tppt)
REVERT: D   97 LYS cc_start: 0.8946 (mmtt) cc_final: 0.7815 (mmtt)
REVERT: H   96 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8504 (mtpt)
  outliers start: 27
  outliers final: 10
  residues processed: 99
  average time/residue: 0.2038
  time to fit residues: 23.8987
Evaluate side-chains
  84 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   96 LYS
Chi-restraints excluded: chain I residue   49 VAL
Chi-restraints excluded: chain J residue   49 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 21 optimal weight:    9.9990
   chunk 46 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 7 optimal weight:    0.4980
   chunk 33 optimal weight:    6.9990
   chunk 35 optimal weight:   10.0000
   chunk 17 optimal weight:    0.7980
   overall best weight:    3.2586

-------------------------------------------------------------------------------
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 = 0.4265 r_free = 0.4265 target = 0.140245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.095620 restraints weight = 4417.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.099208 restraints weight = 2275.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.101528 restraints weight = 1618.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.7786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   4030  Z= 0.273
  Angle     :  0.570   4.245   5446  Z= 0.307
  Chirality :  0.052   0.153    670
  Planarity :  0.002   0.015    664
  Dihedral  :  5.378  15.001    540
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 14.21 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 5.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.72 (0.29), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.83 (0.22), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS E  50 
 PHE   0.007   0.002   PHE B  94 

*********************** 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
  92 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A   46 LYS cc_start: 0.8101 (tptt) cc_final: 0.7478 (mptt)
REVERT: A   83 GLU cc_start: 0.8325 (mp0) cc_final: 0.7637 (mp0)
REVERT: B   46 LYS cc_start: 0.8387 (tttt) cc_final: 0.7768 (tppt)
REVERT: B   97 LYS cc_start: 0.8988 (mttt) cc_final: 0.7952 (mmtt)
REVERT: D   46 LYS cc_start: 0.8632 (tttt) cc_final: 0.7804 (tppt)
REVERT: D   83 GLU cc_start: 0.8430 (mp0) cc_final: 0.7845 (mp0)
REVERT: G   46 LYS cc_start: 0.8474 (tptt) cc_final: 0.8051 (mptt)
REVERT: J   46 LYS cc_start: 0.8502 (tttm) cc_final: 0.8192 (tptt)
  outliers start: 15
  outliers final: 14
  residues processed: 88
  average time/residue: 0.2124
  time to fit residues: 22.1727
Evaluate side-chains
  89 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   52 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain E residue   50 HIS
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain I residue   49 VAL
Chi-restraints excluded: chain J residue   49 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   chunk 30 optimal weight:   30.0000
   chunk 46 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 16 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.135249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.090306 restraints weight = 4570.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.093529 restraints weight = 2567.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.095589 restraints weight = 1875.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.8113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4030  Z= 0.271
  Angle     :  0.557   4.954   5446  Z= 0.298
  Chirality :  0.052   0.154    670
  Planarity :  0.002   0.011    664
  Dihedral  :  5.311  16.360    540
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 13.16 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 5.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.66 (0.31), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.78 (0.23), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS E  50 
 PHE   0.007   0.002   PHE A  94 

*********************** 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
  99 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.437 
Fit side-chains
REVERT: A   83 GLU cc_start: 0.8341 (mp0) cc_final: 0.7661 (mp0)
REVERT: B   46 LYS cc_start: 0.8389 (tttt) cc_final: 0.7650 (tppt)
REVERT: B   97 LYS cc_start: 0.8951 (mttt) cc_final: 0.7918 (mmtt)
REVERT: D   46 LYS cc_start: 0.8591 (tttt) cc_final: 0.7772 (tppt)
REVERT: D   83 GLU cc_start: 0.8497 (mp0) cc_final: 0.7965 (mp0)
REVERT: I   46 LYS cc_start: 0.8222 (tttp) cc_final: 0.7988 (tttp)
REVERT: I   58 LYS cc_start: 0.8891 (mmtp) cc_final: 0.8669 (mmtm)
  outliers start: 20
  outliers final: 20
  residues processed: 90
  average time/residue: 0.2064
  time to fit residues: 22.0866
Evaluate side-chains
  100 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain E residue   50 HIS
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   48 VAL
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 I residue   49 VAL
Chi-restraints excluded: chain I residue   87 SER
Chi-restraints excluded: chain J residue   49 VAL
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   87 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 24 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:    0.5980
   chunk 27 optimal weight:    9.9990
   chunk 19 optimal weight:    8.9990
   chunk 21 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 40 optimal weight:   20.0000
   overall best weight:    3.5186

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.134671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.090094 restraints weight = 4501.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.093278 restraints weight = 2532.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.095378 restraints weight = 1852.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.8398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4030  Z= 0.294
  Angle     :  0.575   4.934   5446  Z= 0.306
  Chirality :  0.053   0.152    670
  Planarity :  0.002   0.012    664
  Dihedral  :  5.278  16.208    540
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 14.74 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.68 (0.31), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.80 (0.23), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS E  50 
 PHE   0.007   0.001   PHE E  94 

*********************** 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
  107 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 83
  time to evaluate  : 0.419 
Fit side-chains
REVERT: A   83 GLU cc_start: 0.8353 (mp0) cc_final: 0.7688 (mp0)
REVERT: B   46 LYS cc_start: 0.8471 (tttt) cc_final: 0.7706 (tppt)
REVERT: B   97 LYS cc_start: 0.9017 (mttt) cc_final: 0.8034 (mmtt)
REVERT: D   46 LYS cc_start: 0.8648 (tttt) cc_final: 0.7825 (tppt)
REVERT: D   83 GLU cc_start: 0.8439 (mp0) cc_final: 0.7919 (mp0)
REVERT: I   58 LYS cc_start: 0.8862 (mmtp) cc_final: 0.8650 (mmtm)
  outliers start: 24
  outliers final: 23
  residues processed: 100
  average time/residue: 0.2055
  time to fit residues: 24.3362
Evaluate side-chains
  105 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
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   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 D residue   59 THR
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   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   48 VAL
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   52 VAL
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 J residue   49 VAL
Chi-restraints excluded: chain J residue   59 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 44 optimal weight:   20.0000
   chunk 42 optimal weight:    5.9990
   chunk 25 optimal weight:   30.0000
   chunk 34 optimal weight:    8.9990
   chunk 9 optimal weight:    0.0770
   chunk 0 optimal weight:   20.0000
   chunk 10 optimal weight:   20.0000
   chunk 20 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    5.4146

-------------------------------------------------------------------------------
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**
C  99 GLN
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.139717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.092646 restraints weight = 4417.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.096129 restraints weight = 2339.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.098478 restraints weight = 1698.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.8618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   4030  Z= 0.439
  Angle     :  0.657   5.503   5446  Z= 0.350
  Chirality :  0.055   0.160    670
  Planarity :  0.002   0.012    664
  Dihedral  :  5.719  17.521    540
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  7.11 %
    Allowed  : 13.95 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.91 (0.30), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.97 (0.23), residues: 530

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

*********************** 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
  111 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 84
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A   83 GLU cc_start: 0.8429 (mp0) cc_final: 0.7745 (mp0)
REVERT: B   46 LYS cc_start: 0.8463 (tttt) cc_final: 0.7676 (tppt)
REVERT: B   97 LYS cc_start: 0.8943 (mttt) cc_final: 0.7940 (mmtt)
REVERT: D   46 LYS cc_start: 0.8600 (tttt) cc_final: 0.7659 (tppt)
REVERT: D   83 GLU cc_start: 0.8579 (mp0) cc_final: 0.8067 (mp0)
REVERT: F   46 LYS cc_start: 0.8373 (tttm) cc_final: 0.8133 (tttm)
REVERT: H   46 LYS cc_start: 0.8672 (tttp) cc_final: 0.8464 (tptt)
REVERT: J   46 LYS cc_start: 0.8317 (tttm) cc_final: 0.8115 (tttp)
  outliers start: 27
  outliers final: 26
  residues processed: 102
  average time/residue: 0.2045
  time to fit residues: 24.8039
Evaluate side-chains
  110 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain B residue   48 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 D residue   59 THR
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   48 VAL
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain H residue   52 VAL
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 J residue   49 VAL
Chi-restraints excluded: chain J residue   59 THR
Chi-restraints excluded: chain J residue   87 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 41 optimal weight:    0.0980
   chunk 40 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 9 optimal weight:    8.9990
   chunk 39 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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**
C  99 GLN
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.146161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.100236 restraints weight = 4288.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.103996 restraints weight = 2187.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.106535 restraints weight = 1547.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.8702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4030  Z= 0.197
  Angle     :  0.562   6.012   5446  Z= 0.296
  Chirality :  0.052   0.148    670
  Planarity :  0.002   0.016    664
  Dihedral  :  4.953  15.674    540
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 17.11 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.64 (0.31), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.23), residues: 530

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

*********************** 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
  101 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.429 
Fit side-chains
REVERT: A   83 GLU cc_start: 0.8291 (mp0) cc_final: 0.7542 (mp0)
REVERT: B   46 LYS cc_start: 0.8451 (tttt) cc_final: 0.7666 (tppt)
REVERT: B   97 LYS cc_start: 0.8957 (mttt) cc_final: 0.7973 (mmmt)
REVERT: D   46 LYS cc_start: 0.8574 (tttt) cc_final: 0.7733 (tppt)
REVERT: H   46 LYS cc_start: 0.8692 (tttp) cc_final: 0.8489 (tptt)
REVERT: J   46 LYS cc_start: 0.8228 (tttm) cc_final: 0.7916 (tttp)
  outliers start: 17
  outliers final: 16
  residues processed: 97
  average time/residue: 0.2243
  time to fit residues: 25.5343
Evaluate side-chains
  100 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain C residue   52 VAL
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   52 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   48 VAL
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 I residue   49 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 14 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   chunk 9 optimal weight:    0.6980
   chunk 26 optimal weight:   10.0000
   chunk 25 optimal weight:   20.0000
   chunk 42 optimal weight:    0.9990
   chunk 38 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 10 optimal weight:   20.0000
   overall best weight:    3.9388

-------------------------------------------------------------------------------
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**
C  99 GLN
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.143365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.097095 restraints weight = 4374.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.100778 restraints weight = 2229.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.103193 restraints weight = 1583.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.8751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   4030  Z= 0.331
  Angle     :  0.613   6.508   5446  Z= 0.324
  Chirality :  0.053   0.154    670
  Planarity :  0.002   0.007    664
  Dihedral  :  5.227  16.511    540
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 16.84 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.75 (0.30), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.85 (0.23), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS E  50 
 PHE   0.007   0.002   PHE E  94 

*********************** 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
  103 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.409 
Fit side-chains
REVERT: A   83 GLU cc_start: 0.8414 (mp0) cc_final: 0.7687 (mp0)
REVERT: B   46 LYS cc_start: 0.8481 (tttt) cc_final: 0.7643 (tppt)
REVERT: B   97 LYS cc_start: 0.8950 (mttt) cc_final: 0.7931 (mmtt)
REVERT: D   46 LYS cc_start: 0.8580 (tttt) cc_final: 0.7699 (tppt)
REVERT: D   98 ASP cc_start: 0.8619 (m-30) cc_final: 0.8239 (m-30)
REVERT: J   46 LYS cc_start: 0.8406 (tttm) cc_final: 0.8188 (tttp)
  outliers start: 19
  outliers final: 19
  residues processed: 97
  average time/residue: 0.2238
  time to fit residues: 25.7193
Evaluate side-chains
  103 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
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   87 SER
Chi-restraints excluded: chain C residue   52 VAL
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   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   48 VAL
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 I residue   49 VAL
Chi-restraints excluded: chain I residue   87 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 5 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 48 optimal weight:    0.4980
   chunk 17 optimal weight:    8.9990
   chunk 3 optimal weight:    6.9990
   chunk 42 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 40 optimal weight:   20.0000
   overall best weight:    1.7182

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.146712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.100763 restraints weight = 4291.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.104497 restraints weight = 2220.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.107009 restraints weight = 1575.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.8820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4030  Z= 0.192
  Angle     :  0.582   7.082   5446  Z= 0.306
  Chirality :  0.052   0.147    670
  Planarity :  0.002   0.018    664
  Dihedral  :  4.829  15.318    540
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 16.84 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 5.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.48 (0.31), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.24), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS E  50 
 PHE   0.004   0.001   PHE G  94 

********************** 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
  106 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.386 
Fit side-chains
REVERT: B   46 LYS cc_start: 0.8500 (tttt) cc_final: 0.7709 (tppt)
REVERT: B   97 LYS cc_start: 0.8954 (mttt) cc_final: 0.7948 (mmtt)
REVERT: D   46 LYS cc_start: 0.8606 (tttt) cc_final: 0.7767 (tppt)
REVERT: J   46 LYS cc_start: 0.8345 (tttm) cc_final: 0.8114 (tttp)
REVERT: J   96 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7936 (ttpt)
  outliers start: 21
  outliers final: 20
  residues processed: 98
  average time/residue: 0.2244
  time to fit residues: 25.7486
Evaluate side-chains
  106 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
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   87 SER
Chi-restraints excluded: chain C residue   52 VAL
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   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   48 VAL
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 I residue   49 VAL
Chi-restraints excluded: chain I residue   87 SER
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 14 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   chunk 34 optimal weight:    6.9990
   chunk 49 optimal weight:   10.0000
   chunk 9 optimal weight:   20.0000
   chunk 24 optimal weight:    8.9990
   chunk 37 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0870
   overall best weight:    4.0166

-------------------------------------------------------------------------------
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**
C  99 GLN
** D  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.143796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.097215 restraints weight = 4293.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.101027 restraints weight = 2208.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.103417 restraints weight = 1570.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.8850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   4030  Z= 0.341
  Angle     :  0.637   7.400   5446  Z= 0.336
  Chirality :  0.054   0.155    670
  Planarity :  0.002   0.023    664
  Dihedral  :  5.160  16.168    540
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.38 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 15.53 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 5.56 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.67 (0.31), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.79 (0.23), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS E  50 
 PHE   0.007   0.002   PHE E  94 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1434.75 seconds
wall clock time: 25 minutes 42.66 seconds (1542.66 seconds total)