Starting phenix.real_space_refine
on Wed Sep 17 04:21:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fh3_50438/09_2025/9fh3_50438.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fh3_50438/09_2025/9fh3_50438.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fh3_50438/09_2025/9fh3_50438.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fh3_50438/09_2025/9fh3_50438.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fh3_50438/09_2025/9fh3_50438.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fh3_50438/09_2025/9fh3_50438.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.300 sd=   1.508
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    1280      2.51       5
     N     360      2.21       5
     O     340      1.98       5
     H    2110      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4100
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "C"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 410
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
    Chain: "A"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 410
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
    Chain: "B"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 410
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
    Chain: "D"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 410
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
    Chain: "E"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 410
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
    Chain: "F"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 410
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
    Chain: "G"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 410
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
    Chain: "H"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 410
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
    Chain: "I"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 410
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
    Chain: "J"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 410
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
  Time building chain proxies: 1.11, per 1000 atoms: 0.27
  Number of scatterers: 4100
  At special positions: 0
  Unit cell: (72.624, 66.096, 44.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     O     340      8.00
     N     360      7.00
     C    1280      6.00
     H    2110      1.00
    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: 0.34
  Conformation dependent library (CDL) restraints added in 95.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  440

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 46.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1 through 4
      removed outlier: 6.427A  pdb=" N   TYR C   1 " --> pdb=" O   GLU A   2 " (cutoff:3.500A)
      removed outlier: 8.310A  pdb=" N   HIS A   4 " --> pdb=" O   TYR C   1 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   VAL C   3 " --> pdb=" O   HIS A   4 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 9
      removed outlier: 6.686A  pdb=" N   LEU C   8 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 21
      removed outlier: 6.833A  pdb=" N   LEU C  19 " --> pdb=" O   GLY A  18 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   MET A  20 " --> pdb=" O   LEU C  19 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   VAL C  21 " --> pdb=" O   MET A  20 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ILE C  16 " --> pdb=" O   ILE E  17 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   LEU E  19 " --> pdb=" O   ILE C  16 " (cutoff:3.500A)
      removed outlier: 7.378A  pdb=" N   GLY C  18 " --> pdb=" O   LEU E  19 " (cutoff:3.500A)
      removed outlier: 10.387A  pdb=" N   VAL E  21 " --> pdb=" O   GLY C  18 " (cutoff:3.500A)
      removed outlier: 8.819A  pdb=" N   MET C  20 " --> pdb=" O   VAL E  21 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ILE E  16 " --> pdb=" O   ILE G  17 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   LEU G  19 " --> pdb=" O   ILE E  16 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   GLY E  18 " --> pdb=" O   LEU G  19 " (cutoff:3.500A)
      removed outlier: 10.407A  pdb=" N   VAL G  21 " --> pdb=" O   GLY E  18 " (cutoff:3.500A)
      removed outlier: 8.873A  pdb=" N   MET E  20 " --> pdb=" O   VAL G  21 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ILE I  16 " --> pdb=" O   ALA G  15 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   ILE G  17 " --> pdb=" O   ILE I  16 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   GLY I  18 " --> pdb=" O   ILE G  17 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 24 through 26
      removed outlier: 6.625A  pdb=" N   VAL C  25 " --> pdb=" O   ILE A  26 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1 through 4
    Processing sheet with id=AA6, first strand: chain 'B' and resid 7 through 9
    Processing sheet with id=AA7, first strand: chain 'B' and resid 15 through 21
      removed outlier: 6.523A  pdb=" N   ILE B  16 " --> pdb=" O   ILE D  17 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   LEU D  19 " --> pdb=" O   ILE B  16 " (cutoff:3.500A)
      removed outlier: 7.385A  pdb=" N   GLY B  18 " --> pdb=" O   LEU D  19 " (cutoff:3.500A)
      removed outlier: 10.415A  pdb=" N   VAL D  21 " --> pdb=" O   GLY B  18 " (cutoff:3.500A)
      removed outlier: 8.813A  pdb=" N   MET B  20 " --> pdb=" O   VAL D  21 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ILE D  16 " --> pdb=" O   ILE F  17 " (cutoff:3.500A)
      removed outlier: 7.680A  pdb=" N   LEU F  19 " --> pdb=" O   ILE D  16 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   GLY D  18 " --> pdb=" O   LEU F  19 " (cutoff:3.500A)
      removed outlier: 10.396A  pdb=" N   VAL F  21 " --> pdb=" O   GLY D  18 " (cutoff:3.500A)
      removed outlier: 8.831A  pdb=" N   MET D  20 " --> pdb=" O   VAL F  21 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   ILE F  16 " --> pdb=" O   ILE H  17 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   LEU H  19 " --> pdb=" O   ILE F  16 " (cutoff:3.500A)
      removed outlier: 7.380A  pdb=" N   GLY F  18 " --> pdb=" O   LEU H  19 " (cutoff:3.500A)
      removed outlier: 10.405A  pdb=" N   VAL H  21 " --> pdb=" O   GLY F  18 " (cutoff:3.500A)
      removed outlier: 8.868A  pdb=" N   MET F  20 " --> pdb=" O   VAL H  21 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ILE H  16 " --> pdb=" O   ILE J  17 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   LEU J  19 " --> pdb=" O   ILE H  16 " (cutoff:3.500A)
      removed outlier: 7.406A  pdb=" N   GLY H  18 " --> pdb=" O   LEU J  19 " (cutoff:3.500A)
      removed outlier: 10.466A  pdb=" N   VAL J  21 " --> pdb=" O   GLY H  18 " (cutoff:3.500A)
      removed outlier: 8.957A  pdb=" N   MET H  20 " --> pdb=" O   VAL J  21 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 24 through 26

    55 hydrogen bonds defined for protein.
    165 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.01

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        0.96 -     1.13: 2110
        1.13 -     1.30: 320
        1.30 -     1.47: 650
        1.47 -     1.64: 1020
        1.64 -     1.81: 20
  Bond restraints: 4120
  Sorted by residual:
  bond pdb=" N   LYS B   7 "
       pdb=" H   LYS B   7 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" CE1 TYR G   1 "
       pdb=" HE1 TYR G   1 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   SER E  11 "
       pdb=" H   SER E  11 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   VAL A   9 "
       pdb=" H   VAL A   9 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.69e+01
  bond pdb=" CD1 TYR I   1 "
       pdb=" HD1 TYR I   1 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.69e+01
  ... (remaining 4115 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 4964
        1.67 -     3.34: 1618
        3.34 -     5.02: 570
        5.02 -     6.69: 288
        6.69 -     8.36: 40
  Bond angle restraints: 7480
  Sorted by residual:
  angle pdb=" N   HIS F   4 "
        pdb=" CA  HIS F   4 "
        pdb=" C   HIS F   4 "
      ideal   model   delta    sigma   weight residual
     109.07  116.86   -7.79 1.52e+00 4.33e-01 2.63e+01
  angle pdb=" N   HIS E   4 "
        pdb=" CA  HIS E   4 "
        pdb=" C   HIS E   4 "
      ideal   model   delta    sigma   weight residual
     109.07  116.84   -7.77 1.52e+00 4.33e-01 2.61e+01
  angle pdb=" N   HIS D   4 "
        pdb=" CA  HIS D   4 "
        pdb=" C   HIS D   4 "
      ideal   model   delta    sigma   weight residual
     109.07  116.73   -7.66 1.52e+00 4.33e-01 2.54e+01
  angle pdb=" N   HIS G   4 "
        pdb=" CA  HIS G   4 "
        pdb=" C   HIS G   4 "
      ideal   model   delta    sigma   weight residual
     109.07  116.59   -7.52 1.52e+00 4.33e-01 2.45e+01
  angle pdb=" N   HIS C   4 "
        pdb=" CA  HIS C   4 "
        pdb=" C   HIS C   4 "
      ideal   model   delta    sigma   weight residual
     109.07  116.59   -7.52 1.52e+00 4.33e-01 2.45e+01
  ... (remaining 7475 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.05: 1578
       13.05 -    26.10: 114
       26.10 -    39.15: 37
       39.15 -    52.20: 46
       52.20 -    65.25: 85
  Dihedral angle restraints: 1860
    sinusoidal: 1040
      harmonic: 820
  Sorted by residual:
  dihedral pdb=" CA  GLU J   2 "
           pdb=" C   GLU J   2 "
           pdb=" N   VAL J   3 "
           pdb=" CA  VAL J   3 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.84   20.16     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  GLU I   2 "
           pdb=" C   GLU I   2 "
           pdb=" N   VAL I   3 "
           pdb=" CA  VAL I   3 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.93   20.07     0      5.00e+00 4.00e-02 1.61e+01
  dihedral pdb=" CA  GLU G   2 "
           pdb=" C   GLU G   2 "
           pdb=" N   VAL G   3 "
           pdb=" CA  VAL G   3 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.90   19.10     0      5.00e+00 4.00e-02 1.46e+01
  ... (remaining 1857 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 133
       0.062 -    0.124: 102
       0.124 -    0.187: 51
       0.187 -    0.249: 15
       0.249 -    0.311: 19
  Chirality restraints: 320
  Sorted by residual:
  chirality pdb=" CA  HIS F   4 "
            pdb=" N   HIS F   4 "
            pdb=" C   HIS F   4 "
            pdb=" CB  HIS F   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.41e+00
  chirality pdb=" CA  HIS D   4 "
            pdb=" N   HIS D   4 "
            pdb=" C   HIS D   4 "
            pdb=" CB  HIS D   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.39e+00
  chirality pdb=" CA  HIS G   4 "
            pdb=" N   HIS G   4 "
            pdb=" C   HIS G   4 "
            pdb=" CB  HIS G   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.35e+00
  ... (remaining 317 not shown)

  Planarity restraints: 600
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B   4 "    0.026 2.00e-02 2.50e+03   4.83e-02 5.26e+01
        pdb=" CG  HIS B   4 "   -0.079 2.00e-02 2.50e+03
        pdb=" ND1 HIS B   4 "   -0.063 2.00e-02 2.50e+03
        pdb=" CD2 HIS B   4 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE1 HIS B   4 "   -0.024 2.00e-02 2.50e+03
        pdb=" NE2 HIS B   4 "    0.005 2.00e-02 2.50e+03
        pdb=" HD1 HIS B   4 "    0.072 2.00e-02 2.50e+03
        pdb=" HD2 HIS B   4 "    0.057 2.00e-02 2.50e+03
        pdb=" HE1 HIS B   4 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A   4 "   -0.025 2.00e-02 2.50e+03   4.69e-02 4.96e+01
        pdb=" CG  HIS A   4 "    0.076 2.00e-02 2.50e+03
        pdb=" ND1 HIS A   4 "    0.062 2.00e-02 2.50e+03
        pdb=" CD2 HIS A   4 "    0.021 2.00e-02 2.50e+03
        pdb=" CE1 HIS A   4 "    0.024 2.00e-02 2.50e+03
        pdb=" NE2 HIS A   4 "   -0.006 2.00e-02 2.50e+03
        pdb=" HD1 HIS A   4 "   -0.071 2.00e-02 2.50e+03
        pdb=" HD2 HIS A   4 "   -0.055 2.00e-02 2.50e+03
        pdb=" HE1 HIS A   4 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS C   4 "   -0.028 2.00e-02 2.50e+03   4.60e-02 4.76e+01
        pdb=" CG  HIS C   4 "    0.077 2.00e-02 2.50e+03
        pdb=" ND1 HIS C   4 "    0.060 2.00e-02 2.50e+03
        pdb=" CD2 HIS C   4 "    0.021 2.00e-02 2.50e+03
        pdb=" CE1 HIS C   4 "    0.021 2.00e-02 2.50e+03
        pdb=" NE2 HIS C   4 "   -0.004 2.00e-02 2.50e+03
        pdb=" HD1 HIS C   4 "   -0.066 2.00e-02 2.50e+03
        pdb=" HD2 HIS C   4 "   -0.053 2.00e-02 2.50e+03
        pdb=" HE1 HIS C   4 "   -0.027 2.00e-02 2.50e+03
  ... (remaining 597 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.35: 750
        2.35 -     2.91: 8713
        2.91 -     3.47: 10675
        3.47 -     4.04: 13547
        4.04 -     4.60: 20008
  Nonbonded interactions: 53693
  Sorted by model distance:
  nonbonded pdb="HE22 GLN D   6 "
            pdb="HG13 ILE F  26 "
     model   vdw
     1.784 2.270
  nonbonded pdb="HE22 GLN C   6 "
            pdb="HG13 ILE E  26 "
     model   vdw
     1.788 2.270
  nonbonded pdb="HE22 GLN E   6 "
            pdb="HG13 ILE G  26 "
     model   vdw
     1.789 2.270
  nonbonded pdb=" O   ILE E  26 "
            pdb=" H   ALA G  27 "
     model   vdw
     1.796 2.450
  nonbonded pdb=" O   ILE F  26 "
            pdb=" H   ALA H  27 "
     model   vdw
     1.797 2.450
  ... (remaining 53688 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  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:             1.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.600
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
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      :  0.011   0.034   2010  Z= 0.728
  Angle     :  2.106   7.791   2690  Z= 1.369
  Chirality :  0.117   0.311    320
  Planarity :  0.009   0.033    330
  Dihedral  : 11.275  36.158    690
  Min Nonbonded Distance : 2.684

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (0.45), residues: 260
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.13 (0.34), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.041   0.012   TYR A   1 
 HIS   0.011   0.005   HIS G   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.01128 ( 2010)
  covalent geometry    : angle       2.10558 ( 2690)
  hydrogen bonds       : bond        0.11610 (   55)
  hydrogen bonds       : angle       7.80585 (  165)

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   17 ILE cc_start: 0.8836 (mp) cc_final: 0.8602 (mp)
REVERT: H   17 ILE cc_start: 0.8924 (mp) cc_final: 0.8621 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0652
  time to fit residues: 6.2128
Evaluate side-chains
  52 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5166 r_free = 0.5166 target = 0.275885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.5571 r_free = 0.5571 target = 0.222610 restraints weight = 13113.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.5620 r_free = 0.5620 target = 0.226194 restraints weight = 5347.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.5649 r_free = 0.5649 target = 0.228038 restraints weight = 2514.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.5664 r_free = 0.5664 target = 0.228963 restraints weight = 1256.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.5672 r_free = 0.5672 target = 0.229521 restraints weight = 666.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.5161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.3823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   2010  Z= 0.192
  Angle     :  0.708   4.954   2690  Z= 0.407
  Chirality :  0.059   0.145    320
  Planarity :  0.002   0.008    330
  Dihedral  :  6.204  14.556    280
  Min Nonbonded Distance : 2.661

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.50 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.37), residues: 260
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.07 (0.28), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR B   1 
 HIS   0.006   0.003   HIS E   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 2010)
  covalent geometry    : angle       0.70829 ( 2690)
  hydrogen bonds       : bond        0.03251 (   55)
  hydrogen bonds       : angle       5.69425 (  165)

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 54
  average time/residue: 0.0613
  time to fit residues: 4.4397
Evaluate side-chains
  47 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    1 TYR
Chi-restraints excluded: chain D residue    1 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 14 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 7 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 4 optimal weight:    8.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 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 = 0.5171 r_free = 0.5171 target = 0.262222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5561 r_free = 0.5561 target = 0.221578 restraints weight = 12737.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.5612 r_free = 0.5612 target = 0.225319 restraints weight = 4996.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.5636 r_free = 0.5636 target = 0.227220 restraints weight = 2257.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.5650 r_free = 0.5650 target = 0.228234 restraints weight = 1109.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.5658 r_free = 0.5658 target = 0.228778 restraints weight = 572.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.5146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.4720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2010  Z= 0.168
  Angle     :  0.614   4.936   2690  Z= 0.362
  Chirality :  0.060   0.138    320
  Planarity :  0.002   0.006    330
  Dihedral  :  5.112  12.550    280
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 22.00 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.51 (0.38), residues: 260
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.38 (0.29), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR I   1 
 HIS   0.007   0.002   HIS C   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 2010)
  covalent geometry    : angle       0.61395 ( 2690)
  hydrogen bonds       : bond        0.03258 (   55)
  hydrogen bonds       : angle       5.47852 (  165)

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    1 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6633 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0607
  time to fit residues: 3.8074
Evaluate side-chains
  44 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    1 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 15 optimal weight:    9.9990
   chunk 9 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 6 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 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 = 0.5141 r_free = 0.5141 target = 0.274296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.5541 r_free = 0.5541 target = 0.221770 restraints weight = 13217.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.5594 r_free = 0.5594 target = 0.224994 restraints weight = 5244.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.5615 r_free = 0.5615 target = 0.226619 restraints weight = 2420.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.5628 r_free = 0.5628 target = 0.227491 restraints weight = 1206.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.5635 r_free = 0.5635 target = 0.227981 restraints weight = 654.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.5152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.5254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2010  Z= 0.208
  Angle     :  0.604   4.891   2690  Z= 0.353
  Chirality :  0.060   0.138    320
  Planarity :  0.002   0.006    330
  Dihedral  :  4.863  11.204    280
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 16.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 21.00 %
    Favored  : 76.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.40), residues: 260
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.43 (0.30), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR I   1 
 HIS   0.005   0.002   HIS C   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 2010)
  covalent geometry    : angle       0.60370 ( 2690)
  hydrogen bonds       : bond        0.03149 (   55)
  hydrogen bonds       : angle       5.43056 (  165)

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.6951 (m-80)
REVERT: F    1 TYR cc_start: 0.7175 (OUTLIER) cc_final: 0.6789 (m-80)
REVERT: H    1 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.6033 (m-80)
  outliers start: 6
  outliers final: 0
  residues processed: 43
  average time/residue: 0.0584
  time to fit residues: 3.4608
Evaluate side-chains
  42 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    1 TYR
Chi-restraints excluded: chain F residue    1 TYR
Chi-restraints excluded: chain H residue    1 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 18 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   chunk 13 optimal weight:    9.9990
   chunk 12 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   chunk 10 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 15 optimal weight:    9.9990
   overall best weight:    3.9188

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 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 = 0.5143 r_free = 0.5143 target = 0.260229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.5510 r_free = 0.5510 target = 0.218876 restraints weight = 13152.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.5553 r_free = 0.5553 target = 0.222463 restraints weight = 5225.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.5582 r_free = 0.5582 target = 0.224446 restraints weight = 2430.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.5600 r_free = 0.5600 target = 0.225476 restraints weight = 1233.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.5608 r_free = 0.5608 target = 0.226015 restraints weight = 649.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.5124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.5576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2010  Z= 0.212
  Angle     :  0.577   4.804   2690  Z= 0.339
  Chirality :  0.060   0.145    320
  Planarity :  0.002   0.007    330
  Dihedral  :  4.727  10.887    280
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 18.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 18.00 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.41), residues: 260
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.45 (0.31), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR J   1 
 HIS   0.005   0.002   HIS B   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 2010)
  covalent geometry    : angle       0.57708 ( 2690)
  hydrogen bonds       : bond        0.03131 (   55)
  hydrogen bonds       : angle       5.41498 (  165)

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 TYR cc_start: 0.7334 (OUTLIER) cc_final: 0.7115 (m-80)
REVERT: F    1 TYR cc_start: 0.7277 (OUTLIER) cc_final: 0.6944 (m-80)
REVERT: G    1 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6829 (m-80)
REVERT: H    1 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.6217 (m-80)
REVERT: I    1 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.6400 (m-80)
  outliers start: 8
  outliers final: 1
  residues processed: 41
  average time/residue: 0.0571
  time to fit residues: 3.2106
Evaluate side-chains
  46 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    1 TYR
Chi-restraints excluded: chain F residue    1 TYR
Chi-restraints excluded: chain G residue    1 TYR
Chi-restraints excluded: chain H residue    1 TYR
Chi-restraints excluded: chain I residue    1 TYR
Chi-restraints excluded: chain J residue    1 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 4 optimal weight:    0.7980
   chunk 8 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   chunk 16 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 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 = 0.5186 r_free = 0.5186 target = 0.264316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.5560 r_free = 0.5560 target = 0.224080 restraints weight = 13382.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.5597 r_free = 0.5597 target = 0.227661 restraints weight = 5156.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.5645 r_free = 0.5645 target = 0.229526 restraints weight = 2364.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.5657 r_free = 0.5657 target = 0.230528 restraints weight = 1162.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5664 r_free = 0.5664 target = 0.231020 restraints weight = 603.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.5181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.5767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   2010  Z= 0.118
  Angle     :  0.503   4.085   2690  Z= 0.295
  Chirality :  0.060   0.138    320
  Planarity :  0.002   0.006    330
  Dihedral  :  4.399  10.178    280
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 23.00 %
    Favored  : 76.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.43), residues: 260
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.22 (0.33), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR E   1 
 HIS   0.004   0.002   HIS B   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 2010)
  covalent geometry    : angle       0.50293 ( 2690)
  hydrogen bonds       : bond        0.02803 (   55)
  hydrogen bonds       : angle       5.20095 (  165)

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G    1 TYR cc_start: 0.7189 (OUTLIER) cc_final: 0.6618 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0556
  time to fit residues: 3.1750
Evaluate side-chains
  40 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue    1 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    0.6980
   chunk 9 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 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 = 0.5204 r_free = 0.5204 target = 0.267123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.5587 r_free = 0.5587 target = 0.227407 restraints weight = 13455.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.5632 r_free = 0.5632 target = 0.231067 restraints weight = 5130.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.5663 r_free = 0.5663 target = 0.232927 restraints weight = 2300.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.5677 r_free = 0.5677 target = 0.233865 restraints weight = 1114.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.5684 r_free = 0.5684 target = 0.234357 restraints weight = 566.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.5199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.5931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   2010  Z= 0.109
  Angle     :  0.486   3.896   2690  Z= 0.285
  Chirality :  0.060   0.136    320
  Planarity :  0.001   0.005    330
  Dihedral  :  4.135   9.493    280
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 21.50 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.45), residues: 260
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.09 (0.34), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR E   1 
 HIS   0.004   0.001   HIS C   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 2010)
  covalent geometry    : angle       0.48618 ( 2690)
  hydrogen bonds       : bond        0.02692 (   55)
  hydrogen bonds       : angle       5.08569 (  165)

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 41
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    1 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.6789 (m-80)
REVERT: G    1 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.6607 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0665
  time to fit residues: 3.7444
Evaluate side-chains
  40 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    1 TYR
Chi-restraints excluded: chain G residue    1 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    7.9990
   chunk 7 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0970
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 0 optimal weight:    0.8980
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 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 = 0.5223 r_free = 0.5223 target = 0.270288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.5625 r_free = 0.5625 target = 0.232242 restraints weight = 13185.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.5657 r_free = 0.5657 target = 0.235181 restraints weight = 5219.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.5680 r_free = 0.5680 target = 0.236681 restraints weight = 2377.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.5691 r_free = 0.5691 target = 0.237448 restraints weight = 1174.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.5698 r_free = 0.5698 target = 0.237848 restraints weight = 609.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.5220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.6068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   2010  Z= 0.081
  Angle     :  0.453   3.543   2690  Z= 0.266
  Chirality :  0.060   0.134    320
  Planarity :  0.001   0.005    330
  Dihedral  :  3.862   9.401    280
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 22.00 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.46), residues: 260
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.06 (0.35), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR F   1 
 HIS   0.005   0.001   HIS C   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00176 ( 2010)
  covalent geometry    : angle       0.45328 ( 2690)
  hydrogen bonds       : bond        0.02548 (   55)
  hydrogen bonds       : angle       4.93865 (  165)

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    1 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.6787 (m-80)
REVERT: G    1 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.6650 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0645
  time to fit residues: 3.6339
Evaluate side-chains
  42 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    1 TYR
Chi-restraints excluded: chain G residue    1 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 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 = 0.5189 r_free = 0.5189 target = 0.265327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.5565 r_free = 0.5565 target = 0.225552 restraints weight = 13360.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.5607 r_free = 0.5607 target = 0.229128 restraints weight = 5145.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.5634 r_free = 0.5634 target = 0.231020 restraints weight = 2333.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.5647 r_free = 0.5647 target = 0.231933 restraints weight = 1146.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.5654 r_free = 0.5654 target = 0.232411 restraints weight = 594.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.5184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.6181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.014   2010  Z= 0.131
  Angle     :  0.483   4.013   2690  Z= 0.285
  Chirality :  0.060   0.134    320
  Planarity :  0.001   0.006    330
  Dihedral  :  3.871   9.906    280
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 22.50 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.46), residues: 260
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.06 (0.35), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR I   1 
 HIS   0.004   0.001   HIS C   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 2010)
  covalent geometry    : angle       0.48346 ( 2690)
  hydrogen bonds       : bond        0.02797 (   55)
  hydrogen bonds       : angle       5.03264 (  165)

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F    1 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6878 (m-80)
REVERT: G    1 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6644 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0613
  time to fit residues: 3.2637
Evaluate side-chains
  41 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    1 TYR
Chi-restraints excluded: chain G residue    1 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 10 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 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 = 0.5184 r_free = 0.5184 target = 0.266431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5569 r_free = 0.5569 target = 0.226518 restraints weight = 13081.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.5612 r_free = 0.5612 target = 0.230021 restraints weight = 5049.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.5640 r_free = 0.5640 target = 0.231868 restraints weight = 2316.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.5652 r_free = 0.5652 target = 0.232785 restraints weight = 1142.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.5660 r_free = 0.5660 target = 0.233276 restraints weight = 596.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.5180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.6247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   2010  Z= 0.110
  Angle     :  0.470   3.816   2690  Z= 0.275
  Chirality :  0.060   0.135    320
  Planarity :  0.001   0.006    330
  Dihedral  :  3.846  10.152    280
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 23.50 %
    Favored  : 75.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.05 (0.47), residues: 260
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.05 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR I   1 
 HIS   0.005   0.001   HIS C   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 2010)
  covalent geometry    : angle       0.46959 ( 2690)
  hydrogen bonds       : bond        0.02689 (   55)
  hydrogen bonds       : angle       4.96913 (  165)

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

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

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  520 Ramachandran restraints generated.
    260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 42
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
REVERT: F    1 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6863 (m-80)
REVERT: G    1 TYR cc_start: 0.7189 (OUTLIER) cc_final: 0.6633 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0732
  time to fit residues: 4.0593
Evaluate side-chains
  41 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    1 TYR
Chi-restraints excluded: chain G residue    1 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 17 optimal weight:    8.9990
   chunk 3 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   chunk 15 optimal weight:    4.9990
   chunk 19 optimal weight:    0.4980
   chunk 6 optimal weight:    8.9990
   chunk 10 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   6 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 = 0.5189 r_free = 0.5189 target = 0.267637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.5581 r_free = 0.5581 target = 0.228086 restraints weight = 13276.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.5621 r_free = 0.5621 target = 0.231567 restraints weight = 5109.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.5644 r_free = 0.5644 target = 0.233373 restraints weight = 2340.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.5659 r_free = 0.5659 target = 0.234305 restraints weight = 1164.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.5666 r_free = 0.5666 target = 0.234815 restraints weight = 606.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.5184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.6355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   2010  Z= 0.091
  Angle     :  0.471   3.592   2690  Z= 0.272
  Chirality :  0.060   0.134    320
  Planarity :  0.001   0.005    330
  Dihedral  :  3.804  10.080    280
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 24.50 %
    Favored  : 74.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.47), residues: 260
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.04 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR F   1 
 HIS   0.005   0.001   HIS C   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 ( 2010)
  covalent geometry    : angle       0.47095 ( 2690)
  hydrogen bonds       : bond        0.02611 (   55)
  hydrogen bonds       : angle       4.91763 (  165)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1259.67 seconds
wall clock time: 22 minutes 6.98 seconds (1326.98 seconds total)