Starting phenix.real_space_refine
on Mon Jan 13 20:23:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x7o_38105/01_2025/8x7o_38105.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x7o_38105/01_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_38105/01_2025/8x7o_38105.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x7o_38105/01_2025/8x7o_38105.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x7o_38105/01_2025/8x7o_38105.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x7o_38105/01_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-5571/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: 2.87, per 1000 atoms: 0.72
  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: 0.94
  Conformation dependent library (CDL) restraints added in 449.1 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: 0.45
  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: 0.84

  Time building geometry restraints manager: 1.09 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:             0.740
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.360
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.200
-------------------------------------------------------------------------------
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  : 0.382 
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: 0.2331
  time to fit residues: 25.3124
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  : 0.441 
-------------------------------------------------------------------------------
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 = 27)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.109456 restraints weight = 4219.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.113708 restraints weight = 2113.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.116315 restraints weight = 1461.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3968
-------------------------------------------------------------------------------
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  : 0.427 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8110 (tttt) cc_final: 0.7381 (tppt)
REVERT: H   96 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8240 (tttm)
REVERT: I   79 GLN cc_start: 0.9329 (tt0) cc_final: 0.9093 (tt0)
  outliers start: 16
  outliers final: 5
  residues processed: 86
  average time/residue: 0.1955
  time to fit residues: 20.3791
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  : 0.386 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 31 optimal weight:    9.9990
   chunk 47 optimal weight:    9.9990
   chunk 11 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 42 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0040
   chunk 28 optimal weight:    4.9990
   overall best weight:    2.0000

-------------------------------------------------------------------------------
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**
** 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 = 0.4323 r_free = 0.4323 target = 0.144659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.101794 restraints weight = 4357.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.105200 restraints weight = 2319.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.107470 restraints weight = 1664.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.6479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4030  Z= 0.196
  Angle     :  0.513   5.034   5446  Z= 0.276
  Chirality :  0.051   0.153    670
  Planarity :  0.002   0.010    664
  Dihedral  :  5.166  14.724    540
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 15.00 %
    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 (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: -3.45 (0.29), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.62 (0.22), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS G  50 
 PHE   0.008   0.002   PHE B  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
  84 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.390 
Fit side-chains
REVERT: A   46 LYS cc_start: 0.8228 (tttt) cc_final: 0.7652 (mptt)
REVERT: B   46 LYS cc_start: 0.8295 (tttt) cc_final: 0.7419 (tppt)
REVERT: D   46 LYS cc_start: 0.8460 (tttt) cc_final: 0.7709 (tppt)
REVERT: F   57 GLU cc_start: 0.8051 (mp0) cc_final: 0.7808 (mp0)
REVERT: J   46 LYS cc_start: 0.8034 (tttt) cc_final: 0.7660 (mptt)
  outliers start: 18
  outliers final: 7
  residues processed: 84
  average time/residue: 0.2262
  time to fit residues: 22.3714
Evaluate side-chains
  71 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   50 HIS
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   49 VAL
Chi-restraints excluded: chain I 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:   20.0000
   chunk 13 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 21 optimal weight:   10.0000
   chunk 46 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 7 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 17 optimal weight:    9.9990
   overall best weight:    3.0986

-------------------------------------------------------------------------------
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**
H  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.139981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.095624 restraints weight = 4418.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.099205 restraints weight = 2256.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.101505 restraints weight = 1598.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.7375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   4030  Z= 0.267
  Angle     :  0.573   4.473   5446  Z= 0.308
  Chirality :  0.051   0.153    670
  Planarity :  0.002   0.014    664
  Dihedral  :  5.417  15.054    540
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 13.95 %
    Favored  : 82.11 %
  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: -3.57 (0.29), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.71 (0.22), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS G  50 
 PHE   0.007   0.001   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
  89 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.414 
Fit side-chains
REVERT: A   46 LYS cc_start: 0.8260 (tttt) cc_final: 0.7686 (mptt)
REVERT: A   83 GLU cc_start: 0.8410 (mp0) cc_final: 0.7665 (mp0)
REVERT: B   46 LYS cc_start: 0.8496 (tttt) cc_final: 0.7713 (tppt)
REVERT: D   46 LYS cc_start: 0.8451 (tttt) cc_final: 0.7694 (tppt)
REVERT: D   83 GLU cc_start: 0.8490 (mp0) cc_final: 0.7912 (mp0)
REVERT: G   46 LYS cc_start: 0.8382 (tptt) cc_final: 0.7973 (mptt)
REVERT: I   96 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.7969 (ttpt)
REVERT: J   46 LYS cc_start: 0.8571 (tttt) cc_final: 0.8030 (mptt)
  outliers start: 15
  outliers final: 11
  residues processed: 86
  average time/residue: 0.2194
  time to fit residues: 22.2400
Evaluate side-chains
  84 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
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 I residue   49 VAL
Chi-restraints excluded: chain I residue   96 LYS
Chi-restraints excluded: chain J residue   49 VAL
Chi-restraints excluded: chain J residue   59 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 43 optimal weight:    7.9990
   chunk 30 optimal weight:   20.0000
   chunk 46 optimal weight:    8.9990
   chunk 9 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 16 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    3.9588

-------------------------------------------------------------------------------
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**
** I  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 = 0.4256 r_free = 0.4256 target = 0.139988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.095354 restraints weight = 4514.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.098764 restraints weight = 2423.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.100872 restraints weight = 1753.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.8021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   4030  Z= 0.328
  Angle     :  0.588   4.955   5446  Z= 0.315
  Chirality :  0.053   0.153    670
  Planarity :  0.002   0.011    664
  Dihedral  :  5.487  16.784    540
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 14.47 %
    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 (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 (0.30), 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   0.001   HIS E  50 
 PHE   0.008   0.002   PHE B  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
  103 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A   83 GLU cc_start: 0.8341 (mp0) cc_final: 0.7695 (mp0)
REVERT: B   46 LYS cc_start: 0.8455 (tttt) cc_final: 0.7673 (tppt)
REVERT: B   83 GLU cc_start: 0.8300 (mp0) cc_final: 0.7817 (mp0)
REVERT: B   97 LYS cc_start: 0.8988 (mttt) cc_final: 0.7965 (mmtt)
REVERT: D   46 LYS cc_start: 0.8562 (tttt) cc_final: 0.7822 (tppt)
REVERT: D   98 ASP cc_start: 0.8760 (m-30) cc_final: 0.8420 (m-30)
REVERT: I   96 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8024 (ttpt)
  outliers start: 20
  outliers final: 18
  residues processed: 98
  average time/residue: 0.2140
  time to fit residues: 24.7237
Evaluate side-chains
  99 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 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 D residue   59 THR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   52 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 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   96 LYS
Chi-restraints excluded: chain J residue   49 VAL
Chi-restraints excluded: chain J residue   59 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.0070
   chunk 24 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   chunk 27 optimal weight:    3.9990
   chunk 19 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9990
   chunk 49 optimal weight:   10.0000
   chunk 40 optimal weight:   20.0000
   overall best weight:    2.8006

-------------------------------------------------------------------------------
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 = 0.4197 r_free = 0.4197 target = 0.136086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.091183 restraints weight = 4468.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.094328 restraints weight = 2545.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.096398 restraints weight = 1868.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.8246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4030  Z= 0.240
  Angle     :  0.543   4.723   5446  Z= 0.289
  Chirality :  0.052   0.152    670
  Planarity :  0.002   0.010    664
  Dihedral  :  5.091  15.250    540
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 15.53 %
    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: -3.59 (0.31), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.73 (0.23), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS I  50 
 PHE   0.006   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
  96 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.394 
Fit side-chains
REVERT: A   83 GLU cc_start: 0.8346 (mp0) cc_final: 0.7634 (mp0)
REVERT: B   46 LYS cc_start: 0.8390 (tttt) cc_final: 0.7614 (tppt)
REVERT: B   83 GLU cc_start: 0.8311 (mp0) cc_final: 0.7878 (mp0)
REVERT: B   97 LYS cc_start: 0.8988 (mttt) cc_final: 0.7996 (mmtt)
REVERT: D   46 LYS cc_start: 0.8556 (tttt) cc_final: 0.7784 (tppt)
REVERT: D   83 GLU cc_start: 0.8460 (mp0) cc_final: 0.7941 (mp0)
REVERT: I   96 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.7982 (ttpt)
  outliers start: 18
  outliers final: 16
  residues processed: 91
  average time/residue: 0.2376
  time to fit residues: 25.2411
Evaluate side-chains
  96 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   52 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 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   96 LYS
Chi-restraints excluded: chain J residue   49 VAL
Chi-restraints excluded: chain J residue   87 SER
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:    1.9990
   chunk 25 optimal weight:   20.0000
   chunk 34 optimal weight:   20.0000
   chunk 9 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 10 optimal weight:   20.0000
   chunk 20 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 13 optimal weight:    8.9990
   chunk 7 optimal weight:    0.0040
   overall best weight:    5.0000

-------------------------------------------------------------------------------
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**
** I  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 = 0.4140 r_free = 0.4140 target = 0.132774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.087918 restraints weight = 4534.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.090981 restraints weight = 2567.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.093117 restraints weight = 1898.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.8510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.029   4030  Z= 0.406
  Angle     :  0.639   5.599   5446  Z= 0.339
  Chirality :  0.054   0.158    670
  Planarity :  0.002   0.011    664
  Dihedral  :  5.566  17.293    540
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  6.58 %
    Allowed  : 14.47 %
    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: -3.86 (0.30), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.23), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B  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
  114 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A   83 GLU cc_start: 0.8402 (mp0) cc_final: 0.7716 (mp0)
REVERT: B   46 LYS cc_start: 0.8444 (tttt) cc_final: 0.7711 (tppt)
REVERT: B   83 GLU cc_start: 0.8428 (mp0) cc_final: 0.8046 (mp0)
REVERT: B   97 LYS cc_start: 0.8984 (mttt) cc_final: 0.7974 (mmtt)
REVERT: D   46 LYS cc_start: 0.8605 (tttt) cc_final: 0.7788 (tppt)
REVERT: D   96 LYS cc_start: 0.8662 (tttm) cc_final: 0.8369 (tttp)
REVERT: I   96 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8019 (ttpt)
  outliers start: 25
  outliers final: 23
  residues processed: 105
  average time/residue: 0.2171
  time to fit residues: 26.6940
Evaluate side-chains
  112 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
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   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 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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 41 optimal weight:    4.9990
   chunk 40 optimal weight:   20.0000
   chunk 2 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 39 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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 = 0.4302 r_free = 0.4302 target = 0.144711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.098646 restraints weight = 4295.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.102374 restraints weight = 2221.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.104750 restraints weight = 1583.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.8637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4030  Z= 0.286
  Angle     :  0.590   5.520   5446  Z= 0.312
  Chirality :  0.053   0.153    670
  Planarity :  0.001   0.008    664
  Dihedral  :  5.118  16.276    540
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 16.58 %
    Favored  : 77.11 %
  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: -3.78 (0.30), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.23), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS I  50 
 PHE   0.007   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
  107 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 83
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A   83 GLU cc_start: 0.8333 (mp0) cc_final: 0.7597 (mp0)
REVERT: B   46 LYS cc_start: 0.8437 (tttt) cc_final: 0.7631 (tppt)
REVERT: B   83 GLU cc_start: 0.8302 (mp0) cc_final: 0.7872 (mp0)
REVERT: B   97 LYS cc_start: 0.8966 (mttt) cc_final: 0.7985 (mmmt)
REVERT: D   46 LYS cc_start: 0.8537 (tttt) cc_final: 0.7746 (tppt)
REVERT: H   46 LYS cc_start: 0.8662 (tttp) cc_final: 0.8442 (tptt)
REVERT: I   96 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.7962 (ttpt)
  outliers start: 24
  outliers final: 22
  residues processed: 99
  average time/residue: 0.2207
  time to fit residues: 25.6088
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  : 0.442 
-------------------------------------------------------------------------------
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 B residue   87 SER
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D 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 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   87 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 46 optimal weight:    9.9990
   chunk 9 optimal weight:    0.0980
   chunk 26 optimal weight:    0.0050
   chunk 25 optimal weight:   20.0000
   chunk 42 optimal weight:    0.0010
   chunk 38 optimal weight:    7.9990
   chunk 24 optimal weight:    8.9990
   chunk 10 optimal weight:   20.0000
   overall best weight:    1.8204

-------------------------------------------------------------------------------
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 = 0.4289 r_free = 0.4289 target = 0.143468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.098232 restraints weight = 4371.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.101961 restraints weight = 2299.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.104265 restraints weight = 1647.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.8732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4030  Z= 0.191
  Angle     :  0.552   6.047   5446  Z= 0.291
  Chirality :  0.052   0.148    670
  Planarity :  0.001   0.014    664
  Dihedral  :  4.814  15.380    540
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 16.84 %
    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: -3.53 (0.31), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.24), 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 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
  101 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.421 
Fit side-chains
REVERT: B   46 LYS cc_start: 0.8434 (tttt) cc_final: 0.7664 (tppt)
REVERT: B   83 GLU cc_start: 0.8227 (mp0) cc_final: 0.7780 (mp0)
REVERT: B   97 LYS cc_start: 0.9010 (mttt) cc_final: 0.8030 (mmmt)
REVERT: D   46 LYS cc_start: 0.8552 (tttt) cc_final: 0.7851 (tppt)
REVERT: I   96 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.7965 (ttpt)
REVERT: J   57 GLU cc_start: 0.8188 (mp0) cc_final: 0.7947 (mp0)
  outliers start: 18
  outliers final: 17
  residues processed: 95
  average time/residue: 0.2272
  time to fit residues: 25.2113
Evaluate side-chains
  100 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
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 D residue   52 VAL
Chi-restraints excluded: chain D 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 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 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 17 optimal weight:    9.9990
   chunk 3 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 32 optimal weight:   10.0000
   chunk 40 optimal weight:   20.0000
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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 = 0.4305 r_free = 0.4305 target = 0.144594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.099023 restraints weight = 4302.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.102750 restraints weight = 2256.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.105120 restraints weight = 1617.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.8793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4030  Z= 0.190
  Angle     :  0.559   5.756   5446  Z= 0.294
  Chirality :  0.052   0.147    670
  Planarity :  0.001   0.017    664
  Dihedral  :  4.726  14.916    540
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 16.84 %
    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: -3.32 (0.32), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.52 (0.24), 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 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
  96 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.435 
Fit side-chains
REVERT: B   46 LYS cc_start: 0.8478 (tttt) cc_final: 0.7683 (tppt)
REVERT: B   83 GLU cc_start: 0.8246 (mp0) cc_final: 0.7760 (mp0)
REVERT: B   97 LYS cc_start: 0.9017 (mttt) cc_final: 0.8025 (mmtt)
REVERT: D   46 LYS cc_start: 0.8507 (tttt) cc_final: 0.7826 (tppt)
REVERT: I   96 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.7901 (ttpt)
REVERT: J   57 GLU cc_start: 0.8195 (mp0) cc_final: 0.7937 (mp0)
  outliers start: 17
  outliers final: 16
  residues processed: 91
  average time/residue: 0.2347
  time to fit residues: 24.9889
Evaluate side-chains
  96 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
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 D 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   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 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   chunk 34 optimal weight:    7.9990
   chunk 49 optimal weight:    7.9990
   chunk 9 optimal weight:    0.6980
   chunk 24 optimal weight:    4.9990
   chunk 37 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   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 = 0.4254 r_free = 0.4254 target = 0.140850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.094720 restraints weight = 4324.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.098354 restraints weight = 2234.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.100813 restraints weight = 1599.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.8838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4030  Z= 0.303
  Angle     :  0.607   5.460   5446  Z= 0.320
  Chirality :  0.053   0.154    670
  Planarity :  0.001   0.007    664
  Dihedral  :  5.096  16.111    540
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 16.32 %
    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: -3.51 (0.31), residues: 530
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.66 (0.24), 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 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1478.48 seconds
wall clock time: 28 minutes 3.56 seconds (1683.56 seconds total)