Starting phenix.real_space_refine
on Sat Jan 18 05:57:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qzm_18778/01_2025/8qzm_18778.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qzm_18778/01_2025/8qzm_18778.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qzm_18778/01_2025/8qzm_18778.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qzm_18778/01_2025/8qzm_18778.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qzm_18778/01_2025/8qzm_18778.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qzm_18778/01_2025/8qzm_18778.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     290      5.49       5
     S      11      5.16       5
     C    6718      2.51       5
     N    2292      2.21       5
     O    2830      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 12141
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 641
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 833
          Classifications: {'peptide': 109}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "D"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "E"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 799
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "G"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 837
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "I"
      Number of atoms: 2988
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2988
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2957
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 189
          Classifications: {'peptide': 24}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 21}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
  Time building chain proxies: 7.17, per 1000 atoms: 0.59
  Number of scatterers: 12141
  At special positions: 0
  Unit cell: (77.926, 121.863, 117.718, 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      11     16.00
     P     290     15.00
     O    2830      8.00
     N    2292      7.00
     C    6718      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: 3.32
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1462

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      69.7% alpha, 2.8% beta
      137 base pairs and 256 stacking pairs defined.
    Time for finding SS restraints: 6.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.680A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.610A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.554A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.560A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 123
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.842A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.586A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.787A  pdb=" N   ILE H  61 " --> pdb=" O   LYS H  57 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 124
      removed outlier: 3.671A  pdb=" N   SER H 112 " --> pdb=" O   LYS H 108 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   SER H 124 " --> pdb=" O   LYS H 120 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.969A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.499A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
      removed outlier: 6.643A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.216A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.396A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    406 hydrogen bonds defined for protein.
    1203 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      355 hydrogen bonds
      710 hydrogen bond angles
      0 basepair planarities
      137 basepair parallelities
      256 stacking parallelities
  Total time for adding SS restraints: 4.45

  Time building geometry restraints manager: 3.65 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2357
        1.33 -     1.45: 4234
        1.45 -     1.57: 5753
        1.57 -     1.69: 578
        1.69 -     1.81: 22
  Bond restraints: 12944
  Sorted by residual:
  bond pdb=" P    DG I  20 "
       pdb=" OP2  DG I  20 "
    ideal  model  delta    sigma   weight residual
    1.480  1.520 -0.040 2.00e-02 2.50e+03 4.03e+00
  bond pdb=" P    DT I -59 "
       pdb=" OP2  DT I -59 "
    ideal  model  delta    sigma   weight residual
    1.480  1.520 -0.040 2.00e-02 2.50e+03 4.00e+00
  bond pdb=" P    DC I  52 "
       pdb=" OP2  DC I  52 "
    ideal  model  delta    sigma   weight residual
    1.480  1.519 -0.039 2.00e-02 2.50e+03 3.81e+00
  bond pdb=" P    DG I  21 "
       pdb=" OP1  DG I  21 "
    ideal  model  delta    sigma   weight residual
    1.480  1.518 -0.038 2.00e-02 2.50e+03 3.66e+00
  bond pdb=" P    DC I  53 "
       pdb=" OP1  DC I  53 "
    ideal  model  delta    sigma   weight residual
    1.480  1.518 -0.038 2.00e-02 2.50e+03 3.64e+00
  ... (remaining 12939 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 18376
        1.93 -     3.85: 309
        3.85 -     5.78: 16
        5.78 -     7.71: 14
        7.71 -     9.64: 2
  Bond angle restraints: 18717
  Sorted by residual:
  angle pdb=" N   GLY H 104 "
        pdb=" CA  GLY H 104 "
        pdb=" C   GLY H 104 "
      ideal   model   delta    sigma   weight residual
     111.02  116.92   -5.90 1.86e+00 2.89e-01 1.00e+01
  angle pdb=" CA  LEU D 101 "
        pdb=" CB  LEU D 101 "
        pdb=" CG  LEU D 101 "
      ideal   model   delta    sigma   weight residual
     116.30  125.94   -9.64 3.50e+00 8.16e-02 7.58e+00
  angle pdb=" C3'  DC I  53 "
        pdb=" C2'  DC I  53 "
        pdb=" C1'  DC I  53 "
      ideal   model   delta    sigma   weight residual
     101.60  105.63   -4.03 1.50e+00 4.44e-01 7.20e+00
  angle pdb=" CB  MET A  90 "
        pdb=" CG  MET A  90 "
        pdb=" SD  MET A  90 "
      ideal   model   delta    sigma   weight residual
     112.70  120.68   -7.98 3.00e+00 1.11e-01 7.08e+00
  angle pdb=" C4   DT I -59 "
        pdb=" C5   DT I -59 "
        pdb=" C7   DT I -59 "
      ideal   model   delta    sigma   weight residual
     122.40  118.56    3.84 1.50e+00 4.44e-01 6.56e+00
  ... (remaining 18712 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.29: 5477
       32.29 -    64.58: 1525
       64.58 -    96.87: 40
       96.87 -   129.16: 0
      129.16 -   161.45: 3
  Dihedral angle restraints: 7045
    sinusoidal: 4780
      harmonic: 2265
  Sorted by residual:
  dihedral pdb=" C4'  DT I -59 "
           pdb=" C3'  DT I -59 "
           pdb=" O3'  DT I -59 "
           pdb=" P    DC I -58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   58.55  161.45     1      3.50e+01 8.16e-04 1.53e+01
  dihedral pdb=" C4'  DG I  20 "
           pdb=" C3'  DG I  20 "
           pdb=" O3'  DG I  20 "
           pdb=" P    DG I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   66.42  153.58     1      3.50e+01 8.16e-04 1.49e+01
  dihedral pdb=" C4'  DC I  52 "
           pdb=" C3'  DC I  52 "
           pdb=" O3'  DC I  52 "
           pdb=" P    DC I  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   69.26  150.74     1      3.50e+01 8.16e-04 1.47e+01
  ... (remaining 7042 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.120: 2113
       0.120 -    0.239: 8
       0.239 -    0.359: 1
       0.359 -    0.478: 0
       0.478 -    0.598: 6
  Chirality restraints: 2128
  Sorted by residual:
  chirality pdb=" P    DC I -58 "
            pdb=" OP1  DC I -58 "
            pdb=" OP2  DC I -58 "
            pdb=" O5'  DC I -58 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.94   -0.60 2.00e-01 2.50e+01 8.94e+00
  chirality pdb=" P    DG I  21 "
            pdb=" OP1  DG I  21 "
            pdb=" OP2  DG I  21 "
            pdb=" O5'  DG I  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.92   -0.58 2.00e-01 2.50e+01 8.34e+00
  chirality pdb=" P    DC I  53 "
            pdb=" OP1  DC I  53 "
            pdb=" OP2  DC I  53 "
            pdb=" O5'  DC I  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.89   -0.55 2.00e-01 2.50e+01 7.52e+00
  ... (remaining 2125 not shown)

  Planarity restraints: 1366
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H 102 "    0.031 5.00e-02 4.00e+02   4.71e-02 3.56e+00
        pdb=" N   PRO H 103 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO H 103 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO H 103 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -55 "   -0.023 2.00e-02 2.50e+03   9.99e-03 2.74e+00
        pdb=" N9   DA I -55 "    0.020 2.00e-02 2.50e+03
        pdb=" C8   DA I -55 "    0.003 2.00e-02 2.50e+03
        pdb=" N7   DA I -55 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DA I -55 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I -55 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I -55 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DA I -55 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I -55 "    0.005 2.00e-02 2.50e+03
        pdb=" N3   DA I -55 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I -55 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  57 "    0.023 2.00e-02 2.50e+03   9.44e-03 2.67e+00
        pdb=" N9   DG I  57 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8   DG I  57 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7   DG I  57 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5   DG I  57 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  57 "    0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  57 "    0.007 2.00e-02 2.50e+03
        pdb=" N1   DG I  57 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I  57 "    0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I  57 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DG I  57 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I  57 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1363 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2319
        2.79 -     3.31: 10898
        3.31 -     3.84: 23587
        3.84 -     4.37: 28097
        4.37 -     4.90: 40245
  Nonbonded interactions: 105146
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU G  61 "
            pdb=" NH1 ARG K 181 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" NE2 GLN E 125 "
            pdb=" OE2 GLU F  53 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" OG1 THR F  30 "
            pdb=" OP2  DC J -12 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   LEU A  92 "
            pdb=" OG  SER A  96 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" NH2 ARG F  35 "
            pdb=" OP2  DG I   8 "
     model   vdw
     2.315 3.120
  ... (remaining 105141 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' and resid 39 through 134)
  selection = (chain 'E' and resid 39 through 134)
}
ncs_group {
  reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 24 through 101))
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and (resid 10 through 117 or (resid 118 and (name N or name CA or nam \ 
e C or name O or name CB ))))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.500
  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:             0.040
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     33.130
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12944  Z= 0.247
  Angle     :  0.600   9.637  18717  Z= 0.350
  Chirality :  0.046   0.598   2128
  Planarity :  0.004   0.047   1366
  Dihedral  : 28.215 161.446   5583
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 11.04 %
    Favored  : 88.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.30), residues: 763
  helix:  1.82 (0.22), residues: 539
  sheet:  None (None), residues: 0
  loop : -0.22 (0.37), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.008   0.001   PHE H  70 
 TYR   0.015   0.001   TYR A  41 
 ARG   0.005   0.000   ARG F  67 

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 136
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  108 LYS cc_start: 0.8726 (ttpt) cc_final: 0.8392 (ttmt)
  outliers start: 2
  outliers final: 1
  residues processed: 136
  average time/residue: 0.4041
  time to fit residues: 69.7913
Evaluate side-chains
  118 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   90 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    6.9990
   chunk 76 optimal weight:    4.9990
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
G  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.057279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.043230 restraints weight = 46087.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 1.75
r_work: 0.2731 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8765
moved from start:          0.1025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12944  Z= 0.228
  Angle     :  0.551   8.288  18717  Z= 0.330
  Chirality :  0.034   0.159   2128
  Planarity :  0.004   0.043   1366
  Dihedral  : 30.405 163.858   4044
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 11.66 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.30), residues: 763
  helix:  2.21 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.22 (0.38), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.012   0.001   TYR H  40 
 ARG   0.003   0.000   ARG K 167 

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.9027 (m-30) cc_final: 0.8756 (t0)
REVERT: A  105 GLU cc_start: 0.7886 (tp30) cc_final: 0.7512 (tp30)
REVERT: C   41 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8255 (tm-30)
REVERT: E   49 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8515 (ptp-170)
REVERT: F   68 ASP cc_start: 0.9001 (m-30) cc_final: 0.8793 (m-30)
REVERT: K  187 ARG cc_start: 0.8649 (tpt-90) cc_final: 0.7938 (tpt-90)
  outliers start: 9
  outliers final: 5
  residues processed: 139
  average time/residue: 0.3822
  time to fit residues: 68.2972
Evaluate side-chains
  127 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 121
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  112 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 80 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
E 125 GLN
G  84 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.056151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.042040 restraints weight = 46558.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 1.77
r_work: 0.2695 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8803
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  12944  Z= 0.303
  Angle     :  0.565   5.844  18717  Z= 0.339
  Chirality :  0.036   0.152   2128
  Planarity :  0.004   0.041   1366
  Dihedral  : 30.495 165.517   4041
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.37 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.37 (0.30), residues: 763
  helix:  2.28 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.36 (0.38), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.012   0.001   PHE A  67 
 TYR   0.011   0.001   TYR A  41 
 ARG   0.004   0.000   ARG D  79 

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.9036 (m-30) cc_final: 0.8694 (t0)
REVERT: C   41 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8066 (tm-30)
REVERT: D   76 GLU cc_start: 0.9250 (mm-30) cc_final: 0.9012 (tp30)
REVERT: D   93 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8133 (mp0)
REVERT: E   49 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8507 (ptp-170)
  outliers start: 11
  outliers final: 7
  residues processed: 136
  average time/residue: 0.3892
  time to fit residues: 67.8865
Evaluate side-chains
  128 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  122 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 82 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 85 optimal weight:    6.9990
   chunk 90 optimal weight:    4.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.056693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.042705 restraints weight = 46689.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.2862 rms_B_bonded: 1.83
r_work: 0.2717 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12944  Z= 0.236
  Angle     :  0.545   5.255  18717  Z= 0.329
  Chirality :  0.034   0.158   2128
  Planarity :  0.003   0.039   1366
  Dihedral  : 30.340 165.071   4041
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.62 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.55 (0.30), residues: 763
  helix:  2.41 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.28 (0.39), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.010   0.001   PHE A  67 
 TYR   0.015   0.001   TYR H  83 
 ARG   0.003   0.000   ARG D  79 

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.879 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.9027 (m-30) cc_final: 0.8699 (t0)
REVERT: C   41 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8279 (tm-30)
REVERT: D   93 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8136 (mp0)
REVERT: E   49 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8524 (ptp-170)
REVERT: K  187 ARG cc_start: 0.8742 (tpt-90) cc_final: 0.7989 (tpt-90)
  outliers start: 13
  outliers final: 10
  residues processed: 139
  average time/residue: 0.3623
  time to fit residues: 65.3802
Evaluate side-chains
  130 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain E residue  124 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 96 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 17 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.057539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.043586 restraints weight = 46815.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 1.83
r_work: 0.2743 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12944  Z= 0.202
  Angle     :  0.534   5.554  18717  Z= 0.322
  Chirality :  0.033   0.154   2128
  Planarity :  0.003   0.036   1366
  Dihedral  : 30.153 164.493   4041
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.86 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.78 (0.30), residues: 763
  helix:  2.54 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.11 (0.39), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.011   0.001   TYR H  83 
 ARG   0.004   0.000   ARG K 181 

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.9020 (m-30) cc_final: 0.8671 (t0)
REVERT: C   41 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8256 (tm-30)
REVERT: C   56 GLU cc_start: 0.8983 (tt0) cc_final: 0.8773 (tt0)
REVERT: D   68 ASP cc_start: 0.9235 (t0) cc_final: 0.8989 (t0)
REVERT: D   76 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8993 (tp30)
REVERT: E   49 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8497 (ptp-170)
REVERT: K  182 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8524 (mm-40)
REVERT: K  187 ARG cc_start: 0.8738 (tpt-90) cc_final: 0.7977 (tpt-90)
  outliers start: 11
  outliers final: 7
  residues processed: 143
  average time/residue: 0.3667
  time to fit residues: 67.8375
Evaluate side-chains
  134 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 126
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  122 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   chunk 99 optimal weight:    0.0030
   chunk 97 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    1.0994

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

Flipped N/Q/H residues before XYZ refinement:
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.057210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.043175 restraints weight = 47238.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.2885 rms_B_bonded: 1.83
r_work: 0.2740 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8761
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12944  Z= 0.216
  Angle     :  0.538   6.125  18717  Z= 0.324
  Chirality :  0.033   0.148   2128
  Planarity :  0.003   0.038   1366
  Dihedral  : 30.174 164.225   4041
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.49 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.85 (0.30), residues: 763
  helix:  2.60 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.08 (0.39), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.018   0.001   TYR H  83 
 ARG   0.004   0.000   ARG K 181 

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 1.090 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.9022 (m-30) cc_final: 0.8697 (t0)
REVERT: C   41 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8256 (tm-30)
REVERT: C   56 GLU cc_start: 0.8976 (tt0) cc_final: 0.8754 (tt0)
REVERT: D   68 ASP cc_start: 0.9228 (t0) cc_final: 0.8846 (t0)
REVERT: E   49 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8512 (ptp-170)
REVERT: F   84 MET cc_start: 0.9076 (tpp) cc_final: 0.8784 (mmm)
REVERT: H   34 LYS cc_start: 0.9381 (mmmm) cc_final: 0.9039 (mmtm)
REVERT: K  187 ARG cc_start: 0.8744 (tpt-90) cc_final: 0.8001 (tpt-90)
  outliers start: 11
  outliers final: 8
  residues processed: 138
  average time/residue: 0.3775
  time to fit residues: 67.1219
Evaluate side-chains
  130 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  122 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   chunk 72 optimal weight:    5.9990
   chunk 85 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 40 optimal weight:    0.5980
   chunk 98 optimal weight:    5.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.055899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.041815 restraints weight = 46653.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.2844 rms_B_bonded: 1.79
r_work: 0.2700 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8799
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  12944  Z= 0.294
  Angle     :  0.567   6.285  18717  Z= 0.339
  Chirality :  0.035   0.155   2128
  Planarity :  0.004   0.035   1366
  Dihedral  : 30.459 164.211   4041
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.33 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.30), residues: 763
  helix:  2.52 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.18 (0.39), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H  49 
 PHE   0.011   0.001   PHE A  67 
 TYR   0.015   0.001   TYR H  83 
 ARG   0.005   0.000   ARG H  99 

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.916 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.9083 (m-30) cc_final: 0.8712 (t0)
REVERT: C   41 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8249 (tm-30)
REVERT: C   56 GLU cc_start: 0.9034 (tt0) cc_final: 0.8788 (tt0)
REVERT: E   49 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8475 (ptp-170)
REVERT: F   84 MET cc_start: 0.9162 (tpp) cc_final: 0.8859 (mmm)
REVERT: H   34 LYS cc_start: 0.9401 (mmmm) cc_final: 0.8999 (mmtm)
REVERT: H   35 GLU cc_start: 0.8381 (mm-30) cc_final: 0.6934 (mm-30)
REVERT: K  187 ARG cc_start: 0.8801 (tpt-90) cc_final: 0.8021 (tpt-90)
  outliers start: 13
  outliers final: 9
  residues processed: 137
  average time/residue: 0.3781
  time to fit residues: 66.4214
Evaluate side-chains
  134 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  122 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 46 optimal weight:    0.6980
   chunk 97 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 98 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 94 optimal weight:    4.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.056053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.041960 restraints weight = 47498.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 1.83
r_work: 0.2683 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  12944  Z= 0.272
  Angle     :  0.561   7.137  18717  Z= 0.336
  Chirality :  0.034   0.153   2128
  Planarity :  0.004   0.037   1366
  Dihedral  : 30.424 163.761   4041
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.80 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.73 (0.30), residues: 763
  helix:  2.52 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.13 (0.39), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.011   0.001   PHE A  67 
 TYR   0.014   0.001   TYR H  83 
 ARG   0.006   0.000   ARG K 181 

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.959 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.9124 (m-30) cc_final: 0.8723 (t0)
REVERT: C   41 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8167 (tm-30)
REVERT: C   56 GLU cc_start: 0.9041 (tt0) cc_final: 0.8772 (tt0)
REVERT: E   49 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8469 (ptp-170)
REVERT: F   84 MET cc_start: 0.9213 (tpp) cc_final: 0.8898 (mmm)
REVERT: H   34 LYS cc_start: 0.9400 (mmmm) cc_final: 0.8994 (mmtm)
REVERT: H   35 GLU cc_start: 0.8405 (mm-30) cc_final: 0.6936 (mm-30)
REVERT: K  187 ARG cc_start: 0.8798 (tpt-90) cc_final: 0.8018 (tpt-90)
  outliers start: 12
  outliers final: 10
  residues processed: 136
  average time/residue: 0.3861
  time to fit residues: 67.6552
Evaluate side-chains
  130 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain E residue  124 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 73 optimal weight:    4.9990
   chunk 87 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 18 optimal weight:    0.2980
   chunk 85 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** 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 = 0.3281 r_free = 0.3281 target = 0.055541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.041504 restraints weight = 47392.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.2813 rms_B_bonded: 1.81
r_work: 0.2669 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8813
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  12944  Z= 0.312
  Angle     :  0.579   7.479  18717  Z= 0.345
  Chirality :  0.035   0.157   2128
  Planarity :  0.004   0.036   1366
  Dihedral  : 30.588 163.727   4041
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.95 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.66 (0.30), residues: 763
  helix:  2.46 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.16 (0.39), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.010   0.001   PHE A  67 
 TYR   0.013   0.001   TYR H  83 
 ARG   0.006   0.000   ARG K 181 

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.964 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.9139 (m-30) cc_final: 0.8732 (t0)
REVERT: C   41 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8171 (tm-30)
REVERT: C   56 GLU cc_start: 0.9067 (tt0) cc_final: 0.8788 (tt0)
REVERT: E   49 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8525 (ptp-170)
REVERT: F   84 MET cc_start: 0.9209 (tpp) cc_final: 0.8877 (mmm)
REVERT: H   34 LYS cc_start: 0.9393 (mmmm) cc_final: 0.8979 (mmtm)
REVERT: H   35 GLU cc_start: 0.8383 (mm-30) cc_final: 0.6868 (mm-30)
REVERT: K  187 ARG cc_start: 0.8804 (tpt-90) cc_final: 0.8020 (tpt-90)
  outliers start: 11
  outliers final: 10
  residues processed: 127
  average time/residue: 0.3952
  time to fit residues: 64.0635
Evaluate side-chains
  128 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain E residue  124 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 70 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 84 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.057135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.043014 restraints weight = 46767.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.2869 rms_B_bonded: 1.81
r_work: 0.2728 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12944  Z= 0.195
  Angle     :  0.545   8.295  18717  Z= 0.327
  Chirality :  0.032   0.155   2128
  Planarity :  0.003   0.036   1366
  Dihedral  : 30.155 162.734   4041
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.95 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.89 (0.30), residues: 763
  helix:  2.61 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.01 (0.40), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.008   0.001   PHE H  70 
 TYR   0.020   0.001   TYR H  83 
 ARG   0.005   0.000   ARG K 181 

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 1.007 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.9084 (m-30) cc_final: 0.8668 (t0)
REVERT: C   41 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8152 (tm-30)
REVERT: C   56 GLU cc_start: 0.8996 (tt0) cc_final: 0.8715 (tt0)
REVERT: D   68 ASP cc_start: 0.9258 (t0) cc_final: 0.8856 (t0)
REVERT: E   49 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8473 (ptp-170)
REVERT: F   84 MET cc_start: 0.9158 (tpp) cc_final: 0.8896 (mmm)
REVERT: H   34 LYS cc_start: 0.9397 (mmmm) cc_final: 0.9002 (mmtm)
REVERT: K  187 ARG cc_start: 0.8772 (tpt-90) cc_final: 0.8014 (tpt-90)
  outliers start: 13
  outliers final: 9
  residues processed: 139
  average time/residue: 0.3820
  time to fit residues: 68.3696
Evaluate side-chains
  132 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  124 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 89 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 8 optimal weight:    0.5980
   chunk 92 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 72 optimal weight:    5.9990
   chunk 93 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
G  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.056413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.042275 restraints weight = 46856.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.2847 rms_B_bonded: 1.85
r_work: 0.2706 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12944  Z= 0.252
  Angle     :  0.564   8.448  18717  Z= 0.335
  Chirality :  0.034   0.154   2128
  Planarity :  0.004   0.036   1366
  Dihedral  : 30.312 162.725   4041
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.11 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.84 (0.30), residues: 763
  helix:  2.58 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.08 (0.40), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.010   0.001   PHE A  67 
 TYR   0.014   0.001   TYR H  83 
 ARG   0.005   0.000   ARG K 181 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4813.37 seconds
wall clock time: 86 minutes 54.56 seconds (5214.56 seconds total)