Starting phenix.real_space_refine
on Tue Feb  3 21:40:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9pkv_71704/02_2026/9pkv_71704.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9pkv_71704/02_2026/9pkv_71704.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9pkv_71704/02_2026/9pkv_71704.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9pkv_71704/02_2026/9pkv_71704.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9pkv_71704/02_2026/9pkv_71704.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9pkv_71704/02_2026/9pkv_71704.cif"
  }
  resolution = 2.72
  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=   0.000 sd=   0.036
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    4349      2.51       5
     N    1175      2.21       5
     O    1511      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7062
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 2028
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 2028
          Classifications: {'peptide': 251}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 240}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "K"
      Number of atoms: 854
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 854
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
          Unresolved non-hydrogen bonds: 62
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 44
    Chain: "P"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 70
          Classifications: {'peptide': 9}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 8}
    Chain: "H"
      Number of atoms: 1570
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 209, 1567
          Classifications: {'peptide': 209}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 194}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
      Conformer: "B"
        Number of residues, atoms: 209, 1567
          Classifications: {'peptide': 209}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 194}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
          bond proxies already assigned to first conformer: 1604
    Chain: "B"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 731
          Classifications: {'peptide': 88}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 84}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "L"
      Number of atoms: 1618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1618
          Classifications: {'peptide': 211}
          Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 198}
    Chain: "A"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 49
          Classifications: {'water': 49}
          Link IDs: {None: 48}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "P"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "H"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 54
          Classifications: {'water': 54}
          Link IDs: {None: 53}
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 15
          Classifications: {'water': 15}
          Link IDs: {None: 14}
    Chain: "L"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 65
          Classifications: {'water': 65}
          Link IDs: {None: 64}
  Time building chain proxies: 1.62, per 1000 atoms: 0.23
  Number of scatterers: 7062
  At special positions: 0
  Unit cell: (60.45, 87.75, 137.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O    1511      8.00
     N    1175      7.00
     C    4349      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 101 " - pdb=" SG  CYS A 164 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 203 " - pdb=" SG  CYS A 259 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  23 " - pdb=" SG  CYS K  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 140 " - pdb=" SG  CYS H 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  25 " - pdb=" SG  CYS B  80 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.03

  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: 0.46
  Conformation dependent library (CDL) restraints added in 369.1 milliseconds
  

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1654

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 21 sheets defined
      12.2% alpha, 45.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 51 through 55
    Processing helix  chain 'A' and resid 59 through 85
      removed outlier: 3.511A  pdb=" N   ALA A  69 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLY A  79 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 150
      removed outlier: 3.836A  pdb=" N   THR A 142 " --> pdb=" O   MET A 138 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   THR A 143 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 162
    Processing helix  chain 'A' and resid 162 through 175
    Processing helix  chain 'A' and resid 175 through 180
    Processing helix  chain 'H' and resid 61 through 64
      removed outlier: 3.659A  pdb=" N   LYS H  64 " --> pdb=" O   PRO H  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 61 through 64'
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'H' and resid 185 through 189
      removed outlier: 3.779A  pdb=" N   LEU H 189 " --> pdb=" O   SER H 186 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 4.150A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 126
    Processing helix  chain 'L' and resid 183 through 187
    Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47
      removed outlier: 5.446A  pdb=" N   GLN A  32 " --> pdb=" O   VAL A  28 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   VAL A  28 " --> pdb=" O   GLN A  32 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL A  34 " --> pdb=" O   GLY A  26 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   CYS A 101 " --> pdb=" O   MET A   5 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ILE A 124 " --> pdb=" O   TYR A 116 " (cutoff:3.500A)
      removed outlier: 5.586A  pdb=" N   TYR A 118 " --> pdb=" O   ASP A 122 " (cutoff:3.500A)
      removed outlier: 5.519A  pdb=" N   ASP A 122 " --> pdb=" O   TYR A 118 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 190
      removed outlier: 3.545A  pdb=" N   ALA A 245 " --> pdb=" O   CYS A 203 " (cutoff:3.500A)
      removed outlier: 5.886A  pdb=" N   PHE A 241 " --> pdb=" O   SER A 207 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 188 through 190
      removed outlier: 3.545A  pdb=" N   ALA A 245 " --> pdb=" O   CYS A 203 " (cutoff:3.500A)
      removed outlier: 5.886A  pdb=" N   PHE A 241 " --> pdb=" O   SER A 207 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 214 through 217
      removed outlier: 3.673A  pdb=" N   LEU A 270 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'K' and resid 4 through 8
    Processing sheet with id=AA6, first strand: chain 'K' and resid 11 through 13
    Processing sheet with id=AA7, first strand: chain 'K' and resid 59 through 61
      removed outlier: 5.383A  pdb=" N   PHE K  48 " --> pdb=" O   ARG K  39 " (cutoff:3.500A)
      removed outlier: 5.807A  pdb=" N   ARG K  39 " --> pdb=" O   PHE K  48 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ALA K  34 " --> pdb=" O   ASP K 100 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   TYR K 111 " --> pdb=" O   ILE K  99 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6
      removed outlier: 5.367A  pdb=" N   GLU H  16 " --> pdb=" O   SER H  82B" (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   SER H  82B" --> pdb=" O   GLU H  16 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLN H  77 " --> pdb=" O   ASP H  72 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.511A  pdb=" N   ALA H  88 " --> pdb=" O   VAL H 109 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   TRP H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   TYR H  50 " --> pdb=" O   TRP H  34 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.511A  pdb=" N   ALA H  88 " --> pdb=" O   VAL H 109 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE H 102 " --> pdb=" O   ARG H  94 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 120 through 124
      removed outlier: 6.119A  pdb=" N   TYR H 176 " --> pdb=" O   ASP H 144 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 120 through 124
      removed outlier: 6.119A  pdb=" N   TYR H 176 " --> pdb=" O   ASP H 144 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 151 through 154
      removed outlier: 4.216A  pdb=" N   TYR H 194 " --> pdb=" O   VAL H 211 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 6 through 11
      removed outlier: 5.661A  pdb=" N   PHE B  62 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 6 through 11
      removed outlier: 5.661A  pdb=" N   PHE B  62 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   SER B  55 " --> pdb=" O   TYR B  63 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 44 through 45
    Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.346A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.579A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'L' and resid 114 through 118
      removed outlier: 5.754A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'L' and resid 144 through 150

    339 hydrogen bonds defined for protein.
    873 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.96

  Time building geometry restraints manager: 0.63 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2209
        1.34 -     1.46: 1612
        1.46 -     1.58: 3186
        1.58 -     1.70: 0
        1.70 -     1.81: 38
  Bond restraints: 7045
  Sorted by residual:
  bond pdb=" N   ASP K  63 "
       pdb=" CA  ASP K  63 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.27e-02 6.20e+03 7.94e+00
  bond pdb=" CA  ALA K  62 "
       pdb=" CB  ALA K  62 "
    ideal  model  delta    sigma   weight residual
    1.530  1.486  0.045 1.69e-02 3.50e+03 6.98e+00
  bond pdb=" CA  SER K  64 "
       pdb=" CB  SER K  64 "
    ideal  model  delta    sigma   weight residual
    1.531  1.487  0.043 1.72e-02 3.38e+03 6.37e+00
  bond pdb=" N   GLN K  66 "
       pdb=" CA  GLN K  66 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.31e-02 5.83e+03 5.54e+00
  bond pdb=" N   VAL K  65 "
       pdb=" CA  VAL K  65 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.025 1.25e-02 6.40e+03 4.06e+00
  ... (remaining 7040 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 9431
        1.62 -     3.25: 123
        3.25 -     4.87: 21
        4.87 -     6.50: 9
        6.50 -     8.12: 2
  Bond angle restraints: 9586
  Sorted by residual:
  angle pdb=" N   SER K  64 "
        pdb=" CA  SER K  64 "
        pdb=" C   SER K  64 "
      ideal   model   delta    sigma   weight residual
     113.20  108.62    4.58 1.21e+00 6.83e-01 1.43e+01
  angle pdb=" N   ARG K  53 "
        pdb=" CA  ARG K  53 "
        pdb=" CB  ARG K  53 "
      ideal   model   delta    sigma   weight residual
     110.70  105.37    5.33 1.49e+00 4.50e-01 1.28e+01
  angle pdb=" CA  ILE K  30 "
        pdb=" CB  ILE K  30 "
        pdb=" CG1 ILE K  30 "
      ideal   model   delta    sigma   weight residual
     110.40  116.20   -5.80 1.70e+00 3.46e-01 1.17e+01
  angle pdb=" CA  ARG K  53 "
        pdb=" CB  ARG K  53 "
        pdb=" CG  ARG K  53 "
      ideal   model   delta    sigma   weight residual
     114.10  120.92   -6.82 2.00e+00 2.50e-01 1.16e+01
  angle pdb=" CA  GLN K  66 "
        pdb=" C   GLN K  66 "
        pdb=" O   GLN K  66 "
      ideal   model   delta    sigma   weight residual
     121.47  117.93    3.54 1.15e+00 7.56e-01 9.47e+00
  ... (remaining 9581 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 3538
       17.96 -    35.92: 451
       35.92 -    53.88: 121
       53.88 -    71.84: 32
       71.84 -    89.80: 11
  Dihedral angle restraints: 4153
    sinusoidal: 1576
      harmonic: 2577
  Sorted by residual:
  dihedral pdb=" CB  CYS H 140 "
           pdb=" SG  CYS H 140 "
           pdb=" SG  CYS H 196 "
           pdb=" CB  CYS H 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  150.39  -57.39     1      1.00e+01 1.00e-02 4.43e+01
  dihedral pdb=" CB  CYS K  23 "
           pdb=" SG  CYS K  23 "
           pdb=" SG  CYS K  97 "
           pdb=" CB  CYS K  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  132.95  -39.95     1      1.00e+01 1.00e-02 2.24e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  92 "
           pdb=" CB  CYS H  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   64.03   28.97     1      1.00e+01 1.00e-02 1.20e+01
  ... (remaining 4150 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 938
       0.063 -    0.127: 114
       0.127 -    0.190: 1
       0.190 -    0.254: 0
       0.254 -    0.317: 1
  Chirality restraints: 1054
  Sorted by residual:
  chirality pdb=" CA  VAL K  65 "
            pdb=" N   VAL K  65 "
            pdb=" C   VAL K  65 "
            pdb=" CB  VAL K  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.76   -0.32 2.00e-01 2.50e+01 2.52e+00
  chirality pdb=" CA  ILE L 106 "
            pdb=" N   ILE L 106 "
            pdb=" C   ILE L 106 "
            pdb=" CB  ILE L 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.18e-01
  chirality pdb=" CA  ILE H 195 "
            pdb=" N   ILE H 195 "
            pdb=" C   ILE H 195 "
            pdb=" CB  ILE H 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  ... (remaining 1051 not shown)

  Planarity restraints: 1225
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 148 "   -0.031 5.00e-02 4.00e+02   4.63e-02 3.42e+00
        pdb=" N   PRO H 149 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO H 149 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO H 149 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE K  30 "   -0.009 2.00e-02 2.50e+03   1.71e-02 2.93e+00
        pdb=" C   ILE K  30 "    0.030 2.00e-02 2.50e+03
        pdb=" O   ILE K  30 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   SER K  31 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 111 "    0.117 9.50e-02 1.11e+02   5.28e-02 2.09e+00
        pdb=" NE  ARG A 111 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 111 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 111 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 111 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1222 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1343
        2.77 -     3.30: 6141
        3.30 -     3.84: 12486
        3.84 -     4.37: 15393
        4.37 -     4.90: 26621
  Nonbonded interactions: 61984
  Sorted by model distance:
  nonbonded pdb=" O   ASP L  82 "
            pdb=" OH  TYR L  86 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   GLU H 101 "
            pdb=" O   HOH H 301 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   TYR H  32 "
            pdb=" O   HOH H 302 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   LEU A 126 "
            pdb=" O   HOH A 401 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OD1 ASP A 122 "
            pdb=" NE1 TRP B  60 "
     model   vdw
     2.245 3.120
  ... (remaining 61979 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.50 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:             4.250
  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:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.400
  Find NCS groups from input model:        0.020
  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:             0.010
  Load rotamer database and sin/cos tables:6.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
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      :  0.003   0.045   7053  Z= 0.140
  Angle     :  0.524   8.121   9602  Z= 0.280
  Chirality :  0.041   0.317   1054
  Planarity :  0.004   0.053   1225
  Dihedral  : 17.933  89.802   2475
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.71 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 31.74 %
    Favored  : 65.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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 are not related in a simple way.
  whole:  0.07 (0.30), residues: 864
  helix: -0.87 (0.57), residues: 85
  sheet:  0.43 (0.29), residues: 376
  loop :  0.04 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 111 
 TYR   0.015   0.001   TYR A  99 
 PHE   0.010   0.001   PHE L  96 
 TRP   0.012   0.001   TRP A 244 
 HIS   0.002   0.001   HIS P   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7045)
  covalent geometry    : angle       0.52356 ( 9586)
  SS BOND              : bond        0.00233 (    8)
  SS BOND              : angle       0.59670 (   16)
  hydrogen bonds       : bond        0.24506 (  292)
  hydrogen bonds       : angle      10.20833 (  873)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.171 
Fit side-chains
REVERT: A   46 GLU cc_start: 0.7554 (mp0) cc_final: 0.7167 (mp0)
REVERT: A   48 ARG cc_start: 0.7019 (mmt90) cc_final: 0.6424 (mmt-90)
REVERT: A  128 GLU cc_start: 0.7411 (tp30) cc_final: 0.6708 (tt0)
REVERT: A  138 MET cc_start: 0.7040 (mmm) cc_final: 0.6601 (mmm)
REVERT: H   82 VAL cc_start: 0.7525 (t) cc_final: 0.7074 (m)
REVERT: H   97 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8353 (mt-10)
REVERT: H  161 SER cc_start: 0.8093 (p) cc_final: 0.7519 (t)
REVERT: H  199 ASN cc_start: 0.7175 (t0) cc_final: 0.6773 (m110)
REVERT: B    3 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7551 (mtt180)
REVERT: B   99 MET cc_start: 0.4918 (mtt) cc_final: 0.4402 (ttp)
  outliers start: 17
  outliers final: 13
  residues processed: 106
  average time/residue: 0.4130
  time to fit residues: 46.4758
Evaluate side-chains
  106 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue   72 SER
Chi-restraints excluded: chain K residue   80 VAL
Chi-restraints excluded: chain H residue   15 SER
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain B residue    3 ARG
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue  105 ASP
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  150 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
K  85 ASN
H  58 ASN
H 171 GLN
H 197 ASN
B  24 ASN
B  31 HIS
B  83 ASN
L  79 GLN
L 124 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.182791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.141370 restraints weight = 6855.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 2.05
r_work: 0.3526 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3431
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3431 r_free = 0.3431    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3431 r_free = 0.3431    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3431
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.0937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7053  Z= 0.166
  Angle     :  0.575   8.407   9602  Z= 0.303
  Chirality :  0.043   0.134   1054
  Planarity :  0.004   0.048   1225
  Dihedral  :  6.248  64.348    990
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 29.16 %
    Favored  : 65.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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 are not related in a simple way.
  whole:  0.12 (0.29), residues: 864
  helix: -0.51 (0.55), residues: 89
  sheet:  0.61 (0.29), residues: 353
  loop : -0.14 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 111 
 TYR   0.018   0.001   TYR A  99 
 PHE   0.012   0.002   PHE A   9 
 TRP   0.012   0.001   TRP A 204 
 HIS   0.003   0.001   HIS P   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 7045)
  covalent geometry    : angle       0.57401 ( 9586)
  SS BOND              : bond        0.00403 (    8)
  SS BOND              : angle       1.01260 (   16)
  hydrogen bonds       : bond        0.04521 (  292)
  hydrogen bonds       : angle       7.00591 (  873)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 93
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 GLU cc_start: 0.7537 (mp0) cc_final: 0.7081 (mp0)
REVERT: A   48 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6553 (mmt-90)
REVERT: A  128 GLU cc_start: 0.7426 (tp30) cc_final: 0.6716 (tt0)
REVERT: A  138 MET cc_start: 0.7027 (mmm) cc_final: 0.6585 (mmm)
REVERT: K   66 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7435 (tt0)
REVERT: H   82 VAL cc_start: 0.7718 (t) cc_final: 0.7348 (m)
REVERT: H   97 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8394 (mt-10)
REVERT: H  161 SER cc_start: 0.8127 (p) cc_final: 0.7550 (t)
REVERT: H  212 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6640 (pm20)
REVERT: B    3 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7456 (mtt180)
REVERT: B   99 MET cc_start: 0.4946 (mtt) cc_final: 0.4448 (ttp)
REVERT: L  161 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7134 (mt-10)
  outliers start: 36
  outliers final: 17
  residues processed: 119
  average time/residue: 0.4893
  time to fit residues: 61.6928
Evaluate side-chains
  111 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ARG
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue   36 SER
Chi-restraints excluded: chain K residue   66 GLN
Chi-restraints excluded: chain K residue   80 VAL
Chi-restraints excluded: chain P residue    1 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  212 GLU
Chi-restraints excluded: chain B residue    3 ARG
Chi-restraints excluded: chain L residue  129 THR
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  150 VAL
Chi-restraints excluded: chain L residue  161 GLU
Chi-restraints excluded: chain L residue  183 LYS
Chi-restraints excluded: chain L residue  206 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 23 optimal weight:    9.9990
   chunk 6 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 83 optimal weight:    8.9990
   chunk 13 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
H  58 ASN
H 197 ASN
B  83 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.181556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.143019 restraints weight = 6778.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 1.81
r_work: 0.3520 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3385 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3429
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3429
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7053  Z= 0.183
  Angle     :  0.577   8.793   9602  Z= 0.299
  Chirality :  0.043   0.133   1054
  Planarity :  0.004   0.046   1225
  Dihedral  :  5.623  49.773    978
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  : 26.98 %
    Favored  : 66.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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 are not related in a simple way.
  whole:  0.08 (0.29), residues: 864
  helix: -0.20 (0.56), residues: 90
  sheet:  0.55 (0.28), residues: 351
  loop : -0.22 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  21 
 TYR   0.019   0.002   TYR A  99 
 PHE   0.013   0.002   PHE L  96 
 TRP   0.015   0.002   TRP A 204 
 HIS   0.004   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 7045)
  covalent geometry    : angle       0.57642 ( 9586)
  SS BOND              : bond        0.00427 (    8)
  SS BOND              : angle       1.01411 (   16)
  hydrogen bonds       : bond        0.03884 (  292)
  hydrogen bonds       : angle       6.33564 (  873)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 96
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 GLU cc_start: 0.7612 (mp0) cc_final: 0.7142 (mp0)
REVERT: A   48 ARG cc_start: 0.6972 (mmt90) cc_final: 0.6381 (mmt-90)
REVERT: A  128 GLU cc_start: 0.7404 (tp30) cc_final: 0.6710 (tm-30)
REVERT: A  138 MET cc_start: 0.6884 (mmm) cc_final: 0.6433 (mmm)
REVERT: H   97 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8386 (mt-10)
REVERT: H  161 SER cc_start: 0.8183 (p) cc_final: 0.7641 (t)
REVERT: H  212 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6550 (pm20)
REVERT: B    3 ARG cc_start: 0.8038 (mtm-85) cc_final: 0.7637 (mtt180)
REVERT: B   50 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.5682 (mm-30)
REVERT: L  161 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7331 (mt-10)
  outliers start: 45
  outliers final: 25
  residues processed: 131
  average time/residue: 0.4012
  time to fit residues: 55.8319
Evaluate side-chains
  121 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue   36 SER
Chi-restraints excluded: chain K residue   65 VAL
Chi-restraints excluded: chain K residue   80 VAL
Chi-restraints excluded: chain K residue  108 SER
Chi-restraints excluded: chain P residue    1 SER
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   70 SER
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  212 GLU
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue  129 THR
Chi-restraints excluded: chain L residue  131 SER
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  150 VAL
Chi-restraints excluded: chain L residue  161 GLU
Chi-restraints excluded: chain L residue  183 LYS
Chi-restraints excluded: chain L residue  191 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 55 optimal weight:    0.7980
   chunk 23 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:   20.0000
   chunk 73 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
H 197 ASN
B  83 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.181416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.142951 restraints weight = 6878.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 1.84
r_work: 0.3517 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3383 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3426
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3426
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.1428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7053  Z= 0.187
  Angle     :  0.578   8.825   9602  Z= 0.300
  Chirality :  0.043   0.133   1054
  Planarity :  0.004   0.047   1225
  Dihedral  :  5.337  44.361    974
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  6.27 %
    Allowed  : 27.25 %
    Favored  : 66.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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 are not related in a simple way.
  whole:  0.01 (0.29), residues: 864
  helix: -0.09 (0.56), residues: 90
  sheet:  0.48 (0.27), residues: 362
  loop : -0.31 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  21 
 TYR   0.019   0.002   TYR A  99 
 PHE   0.013   0.002   PHE L  96 
 TRP   0.011   0.001   TRP A 204 
 HIS   0.003   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 7045)
  covalent geometry    : angle       0.57662 ( 9586)
  SS BOND              : bond        0.00419 (    8)
  SS BOND              : angle       1.03539 (   16)
  hydrogen bonds       : bond        0.03665 (  292)
  hydrogen bonds       : angle       6.14455 (  873)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 98
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 GLU cc_start: 0.7663 (mp0) cc_final: 0.7181 (mp0)
REVERT: A   48 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6347 (mmt-90)
REVERT: A  128 GLU cc_start: 0.7409 (tp30) cc_final: 0.6713 (tm-30)
REVERT: A  138 MET cc_start: 0.6851 (mmm) cc_final: 0.6390 (mmm)
REVERT: A  189 MET cc_start: 0.6343 (ttp) cc_final: 0.6142 (tpp)
REVERT: H   16 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7018 (tt0)
REVERT: H   97 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8374 (mt-10)
REVERT: H  161 SER cc_start: 0.8191 (p) cc_final: 0.7674 (t)
REVERT: H  212 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6540 (pm20)
REVERT: B   50 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.5683 (mm-30)
  outliers start: 46
  outliers final: 28
  residues processed: 133
  average time/residue: 0.3943
  time to fit residues: 55.6975
Evaluate side-chains
  125 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 94
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ARG
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  232 GLU
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue   36 SER
Chi-restraints excluded: chain K residue   65 VAL
Chi-restraints excluded: chain K residue   80 VAL
Chi-restraints excluded: chain K residue  108 SER
Chi-restraints excluded: chain P residue    1 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   70 SER
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  212 GLU
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue  129 THR
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  150 VAL
Chi-restraints excluded: chain L residue  183 LYS
Chi-restraints excluded: chain L residue  191 VAL
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 72 optimal weight:    0.5980
   chunk 47 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
H 197 ASN
B  83 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.180934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.142272 restraints weight = 6858.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 1.83
r_work: 0.3505 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3369 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3415
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3415 r_free = 0.3415    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3415 r_free = 0.3415    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3415
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7053  Z= 0.203
  Angle     :  0.592   8.903   9602  Z= 0.305
  Chirality :  0.043   0.142   1054
  Planarity :  0.004   0.047   1225
  Dihedral  :  5.403  42.974    974
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  6.68 %
    Allowed  : 26.16 %
    Favored  : 67.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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 are not related in a simple way.
  whole:  0.00 (0.29), residues: 864
  helix: -0.00 (0.57), residues: 89
  sheet:  0.50 (0.27), residues: 362
  loop : -0.36 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  21 
 TYR   0.019   0.002   TYR A  99 
 PHE   0.013   0.002   PHE L  96 
 TRP   0.011   0.002   TRP A  60 
 HIS   0.004   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 7045)
  covalent geometry    : angle       0.59042 ( 9586)
  SS BOND              : bond        0.00442 (    8)
  SS BOND              : angle       1.06550 (   16)
  hydrogen bonds       : bond        0.03694 (  292)
  hydrogen bonds       : angle       6.08780 (  873)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 95
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A   46 GLU cc_start: 0.7733 (mp0) cc_final: 0.7147 (mp0)
REVERT: A   48 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.6317 (mmt-90)
REVERT: A  128 GLU cc_start: 0.7448 (tp30) cc_final: 0.6715 (tm-30)
REVERT: A  138 MET cc_start: 0.6798 (mmm) cc_final: 0.6359 (mmm)
REVERT: A  181 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6631 (ptt90)
REVERT: K   66 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7368 (tt0)
REVERT: H   16 GLU cc_start: 0.7740 (mt-10) cc_final: 0.6997 (tt0)
REVERT: H   97 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8393 (mt-10)
REVERT: H  161 SER cc_start: 0.8170 (p) cc_final: 0.7671 (t)
REVERT: H  212 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6534 (pm20)
REVERT: B    3 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7734 (mtt180)
REVERT: B   50 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.5639 (mm-30)
REVERT: L  161 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7126 (mt-10)
  outliers start: 49
  outliers final: 29
  residues processed: 131
  average time/residue: 0.4379
  time to fit residues: 60.8382
Evaluate side-chains
  128 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 93
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ARG
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  181 ARG
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue   36 SER
Chi-restraints excluded: chain K residue   65 VAL
Chi-restraints excluded: chain K residue   66 GLN
Chi-restraints excluded: chain K residue   80 VAL
Chi-restraints excluded: chain K residue  108 SER
Chi-restraints excluded: chain P residue    1 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   70 SER
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  212 GLU
Chi-restraints excluded: chain B residue    4 THR
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue  105 ASP
Chi-restraints excluded: chain L residue  129 THR
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  150 VAL
Chi-restraints excluded: chain L residue  161 GLU
Chi-restraints excluded: chain L residue  191 VAL
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 73 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 51 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 71 optimal weight:    0.4980
   chunk 36 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0050
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
H 197 ASN
B  83 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.182730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.143651 restraints weight = 6905.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 2.06
r_work: 0.3545 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3408 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3437
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3437
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7053  Z= 0.122
  Angle     :  0.526   8.064   9602  Z= 0.272
  Chirality :  0.041   0.134   1054
  Planarity :  0.004   0.047   1225
  Dihedral  :  5.068  40.926    974
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 27.52 %
    Favored  : 67.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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 are not related in a simple way.
  whole:  0.21 (0.29), residues: 864
  helix:  0.19 (0.58), residues: 89
  sheet:  0.62 (0.27), residues: 362
  loop : -0.21 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  21 
 TYR   0.015   0.001   TYR A  99 
 PHE   0.010   0.001   PHE H  78 
 TRP   0.009   0.001   TRP H  34 
 HIS   0.002   0.001   HIS L 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 7045)
  covalent geometry    : angle       0.52547 ( 9586)
  SS BOND              : bond        0.00307 (    8)
  SS BOND              : angle       0.76027 (   16)
  hydrogen bonds       : bond        0.03065 (  292)
  hydrogen bonds       : angle       5.74166 (  873)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 97
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6321 (mmt-90)
REVERT: A  128 GLU cc_start: 0.7454 (tp30) cc_final: 0.6736 (tt0)
REVERT: A  138 MET cc_start: 0.6739 (mmm) cc_final: 0.6298 (mmm)
REVERT: A  266 LEU cc_start: 0.5946 (OUTLIER) cc_final: 0.5651 (mt)
REVERT: K   66 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7317 (tt0)
REVERT: H   16 GLU cc_start: 0.7697 (mt-10) cc_final: 0.6936 (tt0)
REVERT: H   97 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8394 (mt-10)
REVERT: H  161 SER cc_start: 0.8102 (p) cc_final: 0.7571 (t)
REVERT: H  212 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6544 (pm20)
REVERT: B   50 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.5741 (mm-30)
REVERT: B   57 SER cc_start: 0.8038 (OUTLIER) cc_final: 0.7807 (p)
  outliers start: 37
  outliers final: 19
  residues processed: 124
  average time/residue: 0.4860
  time to fit residues: 63.7312
Evaluate side-chains
  115 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ARG
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue   36 SER
Chi-restraints excluded: chain K residue   65 VAL
Chi-restraints excluded: chain K residue   66 GLN
Chi-restraints excluded: chain K residue   80 VAL
Chi-restraints excluded: chain K residue  106 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   70 SER
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  212 GLU
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue  129 THR
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  150 VAL
Chi-restraints excluded: chain L residue  183 LYS
Chi-restraints excluded: chain L residue  191 VAL
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0060
   chunk 75 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 54 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
H  58 ASN
H 197 ASN
B  83 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.183141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.144136 restraints weight = 6912.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.07
r_work: 0.3549 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3411 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3435
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3435 r_free = 0.3435    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3435 r_free = 0.3435    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3435
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7053  Z= 0.122
  Angle     :  0.527   7.931   9602  Z= 0.271
  Chirality :  0.041   0.133   1054
  Planarity :  0.004   0.046   1225
  Dihedral  :  4.897  37.922    973
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 27.38 %
    Favored  : 67.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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 are not related in a simple way.
  whole:  0.27 (0.29), residues: 864
  helix:  0.19 (0.57), residues: 90
  sheet:  0.62 (0.26), residues: 369
  loop : -0.13 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  21 
 TYR   0.015   0.001   TYR A  99 
 PHE   0.010   0.001   PHE L  96 
 TRP   0.009   0.001   TRP A 244 
 HIS   0.002   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7045)
  covalent geometry    : angle       0.52649 ( 9586)
  SS BOND              : bond        0.00312 (    8)
  SS BOND              : angle       0.78702 (   16)
  hydrogen bonds       : bond        0.02997 (  292)
  hydrogen bonds       : angle       5.58941 (  873)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 94
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6401 (mmt-90)
REVERT: A  128 GLU cc_start: 0.7434 (tp30) cc_final: 0.6721 (tt0)
REVERT: A  138 MET cc_start: 0.6684 (mmm) cc_final: 0.6219 (mmm)
REVERT: A  266 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5732 (mt)
REVERT: H   16 GLU cc_start: 0.7641 (mt-10) cc_final: 0.6949 (tt0)
REVERT: H   97 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8383 (mt-10)
REVERT: H  161 SER cc_start: 0.8083 (p) cc_final: 0.7546 (t)
REVERT: H  212 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6559 (pm20)
REVERT: B   50 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.5765 (mm-30)
REVERT: B   57 SER cc_start: 0.8014 (OUTLIER) cc_final: 0.7779 (p)
REVERT: B   99 MET cc_start: 0.4994 (mtt) cc_final: 0.4495 (ttp)
REVERT: L  161 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7202 (mt-10)
  outliers start: 38
  outliers final: 25
  residues processed: 121
  average time/residue: 0.4391
  time to fit residues: 56.4254
Evaluate side-chains
  121 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 90
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ARG
Chi-restraints excluded: chain A residue  121 LYS
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue   36 SER
Chi-restraints excluded: chain K residue   80 VAL
Chi-restraints excluded: chain K residue   84 MET
Chi-restraints excluded: chain K residue  102 ASP
Chi-restraints excluded: chain K residue  106 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   70 SER
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  212 GLU
Chi-restraints excluded: chain B residue    4 THR
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue  129 THR
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  150 VAL
Chi-restraints excluded: chain L residue  161 GLU
Chi-restraints excluded: chain L residue  183 LYS
Chi-restraints excluded: chain L residue  191 VAL
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 41 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0270
   chunk 57 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.4438

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

Flipped N/Q/H residues before XYZ refinement:
H  58 ASN
H 197 ASN
B  83 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.184112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.146028 restraints weight = 6996.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 2.09
r_work: 0.3563 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3424 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3454
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7053  Z= 0.111
  Angle     :  0.525   7.814   9602  Z= 0.271
  Chirality :  0.041   0.157   1054
  Planarity :  0.004   0.047   1225
  Dihedral  :  4.857  38.326    973
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 26.84 %
    Favored  : 67.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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 are not related in a simple way.
  whole:  0.35 (0.29), residues: 864
  helix:  0.25 (0.57), residues: 90
  sheet:  0.67 (0.26), residues: 369
  loop : -0.08 (0.33), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  21 
 TYR   0.015   0.001   TYR A  99 
 PHE   0.010   0.001   PHE H  78 
 TRP   0.009   0.001   TRP A 244 
 HIS   0.002   0.001   HIS B  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 7045)
  covalent geometry    : angle       0.52453 ( 9586)
  SS BOND              : bond        0.00289 (    8)
  SS BOND              : angle       0.72791 (   16)
  hydrogen bonds       : bond        0.02867 (  292)
  hydrogen bonds       : angle       5.51010 (  873)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 92
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 GLU cc_start: 0.7706 (mp0) cc_final: 0.7310 (mp0)
REVERT: A   48 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6276 (mmt-90)
REVERT: A  128 GLU cc_start: 0.7425 (tp30) cc_final: 0.6672 (tt0)
REVERT: A  138 MET cc_start: 0.6596 (mmm) cc_final: 0.6118 (mmm)
REVERT: A  266 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5666 (mt)
REVERT: K   66 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7323 (tt0)
REVERT: H   16 GLU cc_start: 0.7618 (mt-10) cc_final: 0.6905 (tt0)
REVERT: H   97 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8383 (mt-10)
REVERT: H  161 SER cc_start: 0.8009 (p) cc_final: 0.7463 (t)
REVERT: H  212 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6525 (pm20)
REVERT: B   50 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.5687 (mm-30)
REVERT: B   57 SER cc_start: 0.7978 (OUTLIER) cc_final: 0.7742 (p)
REVERT: B   99 MET cc_start: 0.4945 (mtt) cc_final: 0.4443 (ttp)
REVERT: L  161 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7181 (mt-10)
  outliers start: 40
  outliers final: 23
  residues processed: 120
  average time/residue: 0.4685
  time to fit residues: 59.6213
Evaluate side-chains
  119 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 89
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ARG
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain K residue   36 SER
Chi-restraints excluded: chain K residue   65 VAL
Chi-restraints excluded: chain K residue   66 GLN
Chi-restraints excluded: chain K residue   80 VAL
Chi-restraints excluded: chain K residue   84 MET
Chi-restraints excluded: chain K residue  102 ASP
Chi-restraints excluded: chain K residue  106 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   70 SER
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  212 GLU
Chi-restraints excluded: chain B residue    4 THR
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue  129 THR
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  150 VAL
Chi-restraints excluded: chain L residue  161 GLU
Chi-restraints excluded: chain L residue  183 LYS
Chi-restraints excluded: chain L residue  191 VAL
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 75 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0470
   overall best weight:    1.0680

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

Flipped N/Q/H residues before XYZ refinement:
A  72 GLN
K  78 ASN
H  58 ASN
H 197 ASN
B  83 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.181045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.142958 restraints weight = 6934.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 1.97
r_work: 0.3526 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3388 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3433
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3433 r_free = 0.3433    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3433 r_free = 0.3433    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3433
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7053  Z= 0.178
  Angle     :  0.576   8.556   9602  Z= 0.296
  Chirality :  0.043   0.133   1054
  Planarity :  0.004   0.047   1225
  Dihedral  :  4.880  38.712    971
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 27.93 %
    Favored  : 67.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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 are not related in a simple way.
  whole:  0.25 (0.29), residues: 864
  helix:  0.19 (0.57), residues: 91
  sheet:  0.64 (0.26), residues: 367
  loop : -0.19 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  21 
 TYR   0.018   0.002   TYR A  99 
 PHE   0.014   0.002   PHE L  96 
 TRP   0.011   0.001   TRP A 244 
 HIS   0.004   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 7045)
  covalent geometry    : angle       0.57537 ( 9586)
  SS BOND              : bond        0.00407 (    8)
  SS BOND              : angle       1.00815 (   16)
  hydrogen bonds       : bond        0.03350 (  292)
  hydrogen bonds       : angle       5.68933 (  873)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 93
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A   46 GLU cc_start: 0.7775 (mp0) cc_final: 0.7362 (mp0)
REVERT: A   48 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.6240 (mmt-90)
REVERT: A  128 GLU cc_start: 0.7449 (tp30) cc_final: 0.6738 (tt0)
REVERT: A  138 MET cc_start: 0.6704 (mmm) cc_final: 0.6217 (mmm)
REVERT: A  266 LEU cc_start: 0.5980 (OUTLIER) cc_final: 0.5712 (mt)
REVERT: H   16 GLU cc_start: 0.7651 (mt-10) cc_final: 0.6927 (tt0)
REVERT: H   97 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8399 (mt-10)
REVERT: H  161 SER cc_start: 0.8130 (p) cc_final: 0.7627 (t)
REVERT: H  212 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6546 (pm20)
REVERT: B    3 ARG cc_start: 0.8069 (mtm-85) cc_final: 0.7773 (mtt180)
REVERT: B   50 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.5688 (mm-30)
REVERT: L  161 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7201 (mt-10)
  outliers start: 34
  outliers final: 25
  residues processed: 119
  average time/residue: 0.3886
  time to fit residues: 49.1350
Evaluate side-chains
  122 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 92
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ARG
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue   36 SER
Chi-restraints excluded: chain K residue   65 VAL
Chi-restraints excluded: chain K residue   80 VAL
Chi-restraints excluded: chain K residue   84 MET
Chi-restraints excluded: chain K residue  102 ASP
Chi-restraints excluded: chain K residue  106 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   70 SER
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  212 GLU
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue  129 THR
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  150 VAL
Chi-restraints excluded: chain L residue  161 GLU
Chi-restraints excluded: chain L residue  191 VAL
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 83 optimal weight:    8.9990
   chunk 62 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 43 optimal weight:    0.7980
   chunk 19 optimal weight:   10.0000
   chunk 76 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
K  78 ASN
H 197 ASN
B  83 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.180743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.142239 restraints weight = 6912.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 1.88
r_work: 0.3523 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3388 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3421
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3421 r_free = 0.3421    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3421 r_free = 0.3421    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3421
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7053  Z= 0.183
  Angle     :  0.583   8.660   9602  Z= 0.299
  Chirality :  0.043   0.139   1054
  Planarity :  0.004   0.046   1225
  Dihedral  :  4.932  38.832    971
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 28.07 %
    Favored  : 67.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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 are not related in a simple way.
  whole:  0.21 (0.29), residues: 864
  helix:  0.24 (0.58), residues: 90
  sheet:  0.63 (0.27), residues: 367
  loop : -0.25 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  21 
 TYR   0.019   0.002   TYR A  99 
 PHE   0.013   0.002   PHE L  96 
 TRP   0.014   0.001   TRP A 244 
 HIS   0.003   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 7045)
  covalent geometry    : angle       0.58165 ( 9586)
  SS BOND              : bond        0.00420 (    8)
  SS BOND              : angle       1.04944 (   16)
  hydrogen bonds       : bond        0.03362 (  292)
  hydrogen bonds       : angle       5.70865 (  873)

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

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

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1728 Ramachandran restraints generated.
    864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 97
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A   46 GLU cc_start: 0.7779 (mp0) cc_final: 0.7370 (mp0)
REVERT: A   48 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6282 (mmt-90)
REVERT: A  128 GLU cc_start: 0.7472 (tp30) cc_final: 0.6771 (tt0)
REVERT: A  138 MET cc_start: 0.6730 (mmm) cc_final: 0.6251 (mmm)
REVERT: A  266 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.5728 (mt)
REVERT: K   22 SER cc_start: 0.6232 (t) cc_final: 0.5983 (t)
REVERT: H   16 GLU cc_start: 0.7679 (mt-10) cc_final: 0.6963 (tt0)
REVERT: H   97 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8385 (mt-10)
REVERT: H  161 SER cc_start: 0.8148 (p) cc_final: 0.7646 (t)
REVERT: H  212 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6499 (pm20)
REVERT: B    3 ARG cc_start: 0.8063 (mtm-85) cc_final: 0.7774 (mtt180)
REVERT: B   50 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.5728 (mm-30)
REVERT: L  149 LYS cc_start: 0.7134 (mtpt) cc_final: 0.6695 (mtmm)
REVERT: L  161 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7199 (mt-10)
  outliers start: 34
  outliers final: 27
  residues processed: 123
  average time/residue: 0.5114
  time to fit residues: 66.8261
Evaluate side-chains
  127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 95
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ARG
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain K residue   21 LEU
Chi-restraints excluded: chain K residue   36 SER
Chi-restraints excluded: chain K residue   65 VAL
Chi-restraints excluded: chain K residue   78 ASN
Chi-restraints excluded: chain K residue   80 VAL
Chi-restraints excluded: chain K residue   84 MET
Chi-restraints excluded: chain K residue  102 ASP
Chi-restraints excluded: chain K residue  106 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   67 VAL
Chi-restraints excluded: chain H residue   70 SER
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  160 THR
Chi-restraints excluded: chain H residue  183 THR
Chi-restraints excluded: chain H residue  212 GLU
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   57 SER
Chi-restraints excluded: chain B residue   83 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue  129 THR
Chi-restraints excluded: chain L residue  146 VAL
Chi-restraints excluded: chain L residue  150 VAL
Chi-restraints excluded: chain L residue  161 GLU
Chi-restraints excluded: chain L residue  191 VAL
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0050
   chunk 9 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
A 191 HIS
K  78 ASN
H 197 ASN
B  83 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.182217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.143474 restraints weight = 6895.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 1.96
r_work: 0.3539 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3401 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3420
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3420 r_free = 0.3420    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3420 r_free = 0.3420    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3420
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7053  Z= 0.138
  Angle     :  0.556   8.804   9602  Z= 0.285
  Chirality :  0.042   0.138   1054
  Planarity :  0.004   0.046   1225
  Dihedral  :  4.843  38.261    971
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 28.20 %
    Favored  : 67.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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 are not related in a simple way.
  whole:  0.29 (0.29), residues: 864
  helix:  0.21 (0.57), residues: 91
  sheet:  0.65 (0.27), residues: 369
  loop : -0.14 (0.33), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  21 
 TYR   0.016   0.001   TYR A  99 
 PHE   0.011   0.002   PHE L  96 
 TRP   0.016   0.001   TRP A 244 
 HIS   0.003   0.001   HIS B  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7045)
  covalent geometry    : angle       0.55547 ( 9586)
  SS BOND              : bond        0.00325 (    8)
  SS BOND              : angle       0.87972 (   16)
  hydrogen bonds       : bond        0.03122 (  292)
  hydrogen bonds       : angle       5.61446 (  873)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2724.38 seconds
wall clock time: 47 minutes 13.41 seconds (2833.41 seconds total)