Starting phenix.real_space_refine
on Sun May 11 04:11:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8a93_15267/05_2025/8a93_15267.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a93_15267/05_2025/8a93_15267.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8a93_15267/05_2025/8a93_15267.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a93_15267/05_2025/8a93_15267.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a93_15267/05_2025/8a93_15267.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a93_15267/05_2025/8a93_15267.cif"
  }
  resolution = 3.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
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: 6
    Type Number    sf(0)   Gaussians
     P      48      5.49       5
     Mg      2      5.21       5
     S       7      5.16       5
     C    4491      2.51       5
     N    1388      2.21       5
     O    1417      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7353
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2660
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 341, 2652
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 18, 'TRANS': 322}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
      Conformer: "B"
        Number of residues, atoms: 341, 2652
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 18, 'TRANS': 322}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
          bond proxies already assigned to first conformer: 2692
    Chain: "B"
      Number of atoms: 2643
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 340, 2635
          Classifications: {'peptide': 340}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 17, 'TRANS': 322}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
      Conformer: "B"
        Number of residues, atoms: 340, 2635
          Classifications: {'peptide': 340}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 17, 'TRANS': 322}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
          bond proxies already assigned to first conformer: 2673
    Chain: "C"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 81
          Classifications: {'peptide': 13}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'TRANS': 12}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 12
    Chain: "D"
      Number of atoms: 323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 323
          Classifications: {'peptide': 44}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 2, 'TRANS': 41}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "F"
      Number of atoms: 685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 685
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 3, 'TRANS': 86}
    Chain: "X"
      Number of atoms: 426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 426
          Classifications: {'DNA': 21}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 20}
    Chain: "Y"
      Number of atoms: 471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 471
          Classifications: {'DNA': 23}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 22}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 8.24, per 1000 atoms: 1.12
  Number of scatterers: 7353
  At special positions: 0
  Unit cell: (82.56, 99.76, 111.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S       7     16.00
     P      48     15.00
     Mg      2     11.99
     O    1417      8.00
     N    1388      7.00
     C    4491      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.99
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1506

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 8 sheets defined
      51.7% alpha, 14.6% beta
      11 base pairs and 42 stacking pairs defined.
    Time for finding SS restraints: 2.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 47
    Processing helix  chain 'A' and resid 54 through 58
    Processing helix  chain 'A' and resid 100 through 107
    Processing helix  chain 'A' and resid 114 through 122
      removed outlier: 4.173A  pdb=" N   LEU A 118 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 138
      removed outlier: 3.680A  pdb=" N   ARG A 138 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 163
      removed outlier: 3.976A  pdb=" N   ALA A 163 " --> pdb=" O   ALA A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 202
      removed outlier: 3.896A  pdb=" N   TYR A 178 " --> pdb=" O   GLU A 174 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ASP A 180 " --> pdb=" O   ALA A 176 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   GLU A 181 " --> pdb=" O   ARG A 177 " (cutoff:3.500A)
      Proline residue:  A 195  - end of helix
    Processing helix  chain 'A' and resid 220 through 227
    Processing helix  chain 'A' and resid 228 through 236
    Processing helix  chain 'A' and resid 241 through 245
      removed outlier: 3.512A  pdb=" N   ASP A 245 " --> pdb=" O   PRO A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 285
    Processing helix  chain 'A' and resid 300 through 312
    Processing helix  chain 'B' and resid 35 through 47
      removed outlier: 3.541A  pdb=" N   LEU B  47 " --> pdb=" O   ILE B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 105
      removed outlier: 3.876A  pdb=" N   LEU B 104 " --> pdb=" O   SER B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 117
    Processing helix  chain 'B' and resid 118 through 123
    Processing helix  chain 'B' and resid 124 through 138
    Processing helix  chain 'B' and resid 141 through 163
      removed outlier: 3.947A  pdb=" N   ALA B 145 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA B 163 " --> pdb=" O   ALA B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 205
      removed outlier: 4.061A  pdb=" N   GLU B 181 " --> pdb=" O   ARG B 177 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA B 184 " --> pdb=" O   ASP B 180 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ARG B 192 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA B 194 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      Proline residue:  B 195  - end of helix
    Processing helix  chain 'B' and resid 220 through 227
    Processing helix  chain 'B' and resid 228 through 236
    Processing helix  chain 'B' and resid 241 through 245
      removed outlier: 3.530A  pdb=" N   ASP B 245 " --> pdb=" O   PRO B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 260
    Processing helix  chain 'B' and resid 261 through 285
    Processing helix  chain 'B' and resid 300 through 312
    Processing helix  chain 'C' and resid 38 through 49
      removed outlier: 3.636A  pdb=" N   GLU C  47 " --> pdb=" O   ALA C  43 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLY C  48 " --> pdb=" O   GLU C  44 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ILE C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 6 through 17
      removed outlier: 4.170A  pdb=" N   LEU D  10 " --> pdb=" O   SER D   6 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ARG D  16 " --> pdb=" O   ARG D  12 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   LEU D  17 " --> pdb=" O   ALA D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 21 through 34
      removed outlier: 3.656A  pdb=" N   GLN D  26 " --> pdb=" O   PRO D  22 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   PHE D  34 " --> pdb=" O   LEU D  30 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 35 through 47
      removed outlier: 3.713A  pdb=" N   ALA D  41 " --> pdb=" O   GLU D  37 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   LEU D  46 " --> pdb=" O   LEU D  42 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU D  47 " --> pdb=" O   ALA D  43 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 85 through 96
      removed outlier: 3.772A  pdb=" N   SER F  95 " --> pdb=" O   ALA F  91 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY F  96 " --> pdb=" O   LEU F  92 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 121 through 126
    Processing helix  chain 'F' and resid 127 through 129
      No H-bonds generated for 'chain 'F' and resid 127 through 129'
    Processing helix  chain 'F' and resid 142 through 160
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 9
      removed outlier: 5.337A  pdb=" N   LEU A   3 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   GLU A  73 " --> pdb=" O   LEU A   3 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 113
      removed outlier: 3.600A  pdb=" N   LEU A 319 " --> pdb=" O   SER A  26 " (cutoff:3.500A)
      removed outlier: 9.002A  pdb=" N   CYS A 331 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ALA A  27 " --> pdb=" O   CYS A 331 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   VAL A 333 " --> pdb=" O   ALA A  27 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   VAL A  29 " --> pdb=" O   VAL A 333 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94
      removed outlier: 4.400A  pdb=" N   VAL A  92 " --> pdb=" O   VAL A  99 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LYS A  97 " --> pdb=" O   LEU A  94 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 214
      removed outlier: 3.613A  pdb=" N   ASP A 246 " --> pdb=" O   GLU A 214 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 9
      removed outlier: 6.137A  pdb=" N   LEU B   3 " --> pdb=" O   GLU B  73 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   GLU B  73 " --> pdb=" O   LEU B   3 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU B  93 " --> pdb=" O   GLU B  82 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 113
      removed outlier: 6.186A  pdb=" N   VAL B 111 " --> pdb=" O   LEU B 291 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   ASP B 293 " --> pdb=" O   VAL B 111 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   VAL B 113 " --> pdb=" O   ASP B 293 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   LEU B 290 " --> pdb=" O   GLN B 316 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   GLY B  24 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   LEU B 319 " --> pdb=" O   GLY B  24 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   SER B  26 " --> pdb=" O   LEU B 319 " (cutoff:3.500A)
      removed outlier: 8.340A  pdb=" N   GLY B 321 " --> pdb=" O   SER B  26 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   LEU B  28 " --> pdb=" O   GLY B 321 " (cutoff:3.500A)
      removed outlier: 9.037A  pdb=" N   CYS B 331 " --> pdb=" O   LEU B  25 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ALA B  27 " --> pdb=" O   CYS B 331 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   VAL B 333 " --> pdb=" O   ALA B  27 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   VAL B  29 " --> pdb=" O   VAL B 333 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 209 through 214
      removed outlier: 3.533A  pdb=" N   ASP B 246 " --> pdb=" O   GLU B 214 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 101 through 104
      removed outlier: 6.135A  pdb=" N   ALA F  81 " --> pdb=" O   HIS F 103 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   LEU F  80 " --> pdb=" O   VAL F 136 " (cutoff:3.500A)

    337 hydrogen bonds defined for protein.
    959 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      27 hydrogen bonds
      54 hydrogen bond angles
      0 basepair planarities
      11 basepair parallelities
      42 stacking parallelities
  Total time for adding SS restraints: 2.31

  Time building geometry restraints manager: 2.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2126
        1.33 -     1.45: 1259
        1.45 -     1.57: 4084
        1.57 -     1.69: 94
        1.69 -     1.81: 10
  Bond restraints: 7573
  Sorted by residual:
  bond pdb=" N3B ANP B 901 "
       pdb=" PG  ANP B 901 "
    ideal  model  delta    sigma   weight residual
    1.795  1.629  0.166 2.00e-02 2.50e+03 6.86e+01
  bond pdb=" N3B ANP A 901 "
       pdb=" PG  ANP A 901 "
    ideal  model  delta    sigma   weight residual
    1.795  1.631  0.164 2.00e-02 2.50e+03 6.73e+01
  bond pdb=" O3A ANP B 901 "
       pdb=" PB  ANP B 901 "
    ideal  model  delta    sigma   weight residual
    1.700  1.622  0.078 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" O3A ANP A 901 "
       pdb=" PB  ANP A 901 "
    ideal  model  delta    sigma   weight residual
    1.700  1.622  0.078 2.00e-02 2.50e+03 1.50e+01
  bond pdb=" O5' ANP B 901 "
       pdb=" PA  ANP B 901 "
    ideal  model  delta    sigma   weight residual
    1.655  1.593  0.062 2.00e-02 2.50e+03 9.63e+00
  ... (remaining 7568 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 10317
        2.20 -     4.40: 107
        4.40 -     6.60: 15
        6.60 -     8.80: 5
        8.80 -    11.01: 2
  Bond angle restraints: 10446
  Sorted by residual:
  angle pdb=" O1B ANP A 901 "
        pdb=" PB  ANP A 901 "
        pdb=" O3A ANP A 901 "
      ideal   model   delta    sigma   weight residual
     103.40  114.41  -11.01 3.00e+00 1.11e-01 1.35e+01
  angle pdb=" O1B ANP B 901 "
        pdb=" PB  ANP B 901 "
        pdb=" O3A ANP B 901 "
      ideal   model   delta    sigma   weight residual
     103.40  114.37  -10.97 3.00e+00 1.11e-01 1.34e+01
  angle pdb=" PA  ANP A 901 "
        pdb=" O3A ANP A 901 "
        pdb=" PB  ANP A 901 "
      ideal   model   delta    sigma   weight residual
     125.41  133.35   -7.94 3.00e+00 1.11e-01 7.01e+00
  angle pdb=" PA  ANP B 901 "
        pdb=" O3A ANP B 901 "
        pdb=" PB  ANP B 901 "
      ideal   model   delta    sigma   weight residual
     125.41  133.13   -7.72 3.00e+00 1.11e-01 6.61e+00
  angle pdb=" CB  LYS F 118 "
        pdb=" CG  LYS F 118 "
        pdb=" CD  LYS F 118 "
      ideal   model   delta    sigma   weight residual
     111.30  117.18   -5.88 2.30e+00 1.89e-01 6.53e+00
  ... (remaining 10441 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3752
       17.95 -    35.89: 460
       35.89 -    53.84: 237
       53.84 -    71.79: 29
       71.79 -    89.73: 10
  Dihedral angle restraints: 4488
    sinusoidal: 2139
      harmonic: 2349
  Sorted by residual:
  dihedral pdb=" CG  ARG B 191 "
           pdb=" CD  ARG B 191 "
           pdb=" NE  ARG B 191 "
           pdb=" CZ  ARG B 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.98  -44.98     2      1.50e+01 4.44e-03 1.07e+01
  dihedral pdb=" CB  GLU A  17 "
           pdb=" CG  GLU A  17 "
           pdb=" CD  GLU A  17 "
           pdb=" OE1 GLU A  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.73  -89.73     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CA  GLU B 294 "
           pdb=" C   GLU B 294 "
           pdb=" N   TRP B 295 "
           pdb=" CA  TRP B 295 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.73  -16.27     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 4485 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1056
       0.057 -    0.113: 112
       0.113 -    0.170: 4
       0.170 -    0.227: 0
       0.227 -    0.283: 2
  Chirality restraints: 1174
  Sorted by residual:
  chirality pdb=" C3' ANP B 901 "
            pdb=" C2' ANP B 901 "
            pdb=" C4' ANP B 901 "
            pdb=" O3' ANP B 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.64    0.28 2.00e-01 2.50e+01 2.01e+00
  chirality pdb=" C3' ANP A 901 "
            pdb=" C2' ANP A 901 "
            pdb=" C4' ANP A 901 "
            pdb=" O3' ANP A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.64    0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" CA  VAL F 161 "
            pdb=" N   VAL F 161 "
            pdb=" C   VAL F 161 "
            pdb=" CB  VAL F 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.15 2.00e-01 2.50e+01 5.98e-01
  ... (remaining 1171 not shown)

  Planarity restraints: 1203
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 114 "    0.021 5.00e-02 4.00e+02   3.14e-02 1.57e+00
        pdb=" N   PRO A 115 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 115 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 115 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 123 "    0.021 5.00e-02 4.00e+02   3.12e-02 1.56e+00
        pdb=" N   PRO A 124 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 124 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 124 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 107 "    0.020 5.00e-02 4.00e+02   3.06e-02 1.50e+00
        pdb=" N   PRO A 108 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 108 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 108 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1200 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 57
        2.64 -     3.20: 5862
        3.20 -     3.77: 10406
        3.77 -     4.33: 13926
        4.33 -     4.90: 22994
  Nonbonded interactions: 53245
  Sorted by model distance:
  nonbonded pdb=" O2G ANP B 901 "
            pdb="MG    MG B 902 "
     model   vdw
     2.072 2.170
  nonbonded pdb=" OG1 THR B  37 "
            pdb="MG    MG B 902 "
     model   vdw
     2.078 2.170
  nonbonded pdb=" O1B ANP B 901 "
            pdb="MG    MG B 902 "
     model   vdw
     2.115 2.170
  nonbonded pdb=" O1B ANP A 901 "
            pdb="MG    MG A 902 "
     model   vdw
     2.132 2.170
  nonbonded pdb=" O2G ANP A 901 "
            pdb="MG    MG A 902 "
     model   vdw
     2.145 2.170
  ... (remaining 53240 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 51 or resid 53 through 72 or (resid 73 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 74 through 96 or (resid \ 
 97 and (name N or name CA or name C or name O or name CB )) or resid 98 through \ 
 140 or (resid 141 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 142 through 165 or (resid 166 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 167 through 191 or resid 193 through 197 or resid 199 throu \ 
gh 341 or resid 901 through 902))
  selection = (chain 'B' and (resid 1 through 49 or (resid 50 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 51 through 191 or resid 193 through 197 or res \ 
id 199 through 285 or (resid 286 and (name N or name CA or name C or name O or n \ 
ame CB )) or resid 287 through 341 or resid 901 through 902))
}

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:             10.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.080
  Process input model:                     25.630
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
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      :  0.005   0.166   7573  Z= 0.224
  Angle     :  0.574  11.006  10446  Z= 0.271
  Chirality :  0.036   0.283   1174
  Planarity :  0.004   0.035   1203
  Dihedral  : 18.984  89.732   2982
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  0.00 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.31), residues: 818
  helix:  2.68 (0.28), residues: 355
  sheet:  0.94 (0.42), residues: 148
  loop : -1.14 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 105 
 HIS   0.003   0.001   HIS A 277 
 PHE   0.008   0.001   PHE D  34 
 TYR   0.004   0.001   TYR B 178 
 ARG   0.008   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21551 (  364)
  hydrogen bonds       : angle       5.98818 ( 1013)
  covalent geometry    : bond        0.00457 ( 7573)
  covalent geometry    : angle       0.57436 (10446)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
REVERT: D   16 ARG cc_start: 0.8284 (mtm110) cc_final: 0.7720 (ptm-80)
  outliers start: 1
  outliers final: 0
  residues processed: 86
  average time/residue: 0.2867
  time to fit residues: 30.8404
Evaluate side-chains
  71 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 78 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.101380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.073022 restraints weight = 31052.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 4.61
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3003
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3003 r_free = 0.3003    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3003 r_free = 0.3003    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3003
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.1065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7573  Z= 0.173
  Angle     :  0.586   7.354  10446  Z= 0.305
  Chirality :  0.039   0.146   1174
  Planarity :  0.004   0.040   1203
  Dihedral  : 19.767  88.504   1458
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  6.70 %
    Favored  : 92.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.30), residues: 818
  helix:  2.44 (0.27), residues: 369
  sheet:  1.40 (0.43), residues: 146
  loop : -1.38 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 105 
 HIS   0.007   0.001   HIS A 277 
 PHE   0.011   0.001   PHE A 193 
 TYR   0.008   0.001   TYR B  79 
 ARG   0.003   0.000   ARG A 157 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05473 (  364)
  hydrogen bonds       : angle       4.24828 ( 1013)
  covalent geometry    : bond        0.00400 ( 7573)
  covalent geometry    : angle       0.58598 (10446)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.713 
Fit side-chains
REVERT: A  102 ARG cc_start: 0.8055 (mtm-85) cc_final: 0.7733 (mtm-85)
REVERT: B  173 ARG cc_start: 0.8266 (mtm-85) cc_final: 0.7915 (mtt90)
  outliers start: 4
  outliers final: 2
  residues processed: 79
  average time/residue: 0.2949
  time to fit residues: 28.7787
Evaluate side-chains
  72 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain C residue   49 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0040
   chunk 50 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.102830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.075922 restraints weight = 20350.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 3.71
r_work: 0.2879 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2882
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2882 r_free = 0.2882    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2882
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.1206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7573  Z= 0.122
  Angle     :  0.505   6.579  10446  Z= 0.263
  Chirality :  0.036   0.130   1174
  Planarity :  0.004   0.045   1203
  Dihedral  : 19.343  88.094   1458
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  9.09 %
    Favored  : 89.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.30), residues: 818
  helix:  2.54 (0.27), residues: 370
  sheet:  1.62 (0.43), residues: 148
  loop : -1.30 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 105 
 HIS   0.003   0.001   HIS A 277 
 PHE   0.010   0.001   PHE D  34 
 TYR   0.006   0.001   TYR B  79 
 ARG   0.006   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04531 (  364)
  hydrogen bonds       : angle       3.93976 ( 1013)
  covalent geometry    : bond        0.00270 ( 7573)
  covalent geometry    : angle       0.50522 (10446)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.774 
Fit side-chains
REVERT: A  102 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.8194 (mtm-85)
  outliers start: 3
  outliers final: 2
  residues processed: 78
  average time/residue: 0.3080
  time to fit residues: 29.4771
Evaluate side-chains
  71 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 69
  time to evaluate  : 1.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain D residue    6 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 66 optimal weight:    0.1980
   chunk 74 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0050
   chunk 30 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.104080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.075145 restraints weight = 40336.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 5.27
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3037
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3037 r_free = 0.3037    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3037
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7573  Z= 0.112
  Angle     :  0.496   6.398  10446  Z= 0.255
  Chirality :  0.035   0.127   1174
  Planarity :  0.004   0.046   1203
  Dihedral  : 19.115  83.205   1458
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  9.73 %
    Favored  : 89.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.30), residues: 818
  helix:  2.64 (0.27), residues: 370
  sheet:  1.75 (0.43), residues: 148
  loop : -1.21 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 105 
 HIS   0.003   0.001   HIS A 257 
 PHE   0.008   0.001   PHE D  34 
 TYR   0.006   0.001   TYR B  79 
 ARG   0.005   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04023 (  364)
  hydrogen bonds       : angle       3.78356 ( 1013)
  covalent geometry    : bond        0.00247 ( 7573)
  covalent geometry    : angle       0.49605 (10446)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.692 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 82
  average time/residue: 0.2954
  time to fit residues: 29.8058
Evaluate side-chains
  77 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain D residue   17 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0020
   chunk 50 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.103228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.074944 restraints weight = 30078.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 4.56
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3036
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3036
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7573  Z= 0.128
  Angle     :  0.509   6.821  10446  Z= 0.262
  Chirality :  0.036   0.156   1174
  Planarity :  0.004   0.045   1203
  Dihedral  : 19.056  80.945   1458
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  9.89 %
    Favored  : 88.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.30), residues: 818
  helix:  2.66 (0.27), residues: 370
  sheet:  1.77 (0.43), residues: 148
  loop : -1.19 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 105 
 HIS   0.005   0.001   HIS A 277 
 PHE   0.009   0.001   PHE A 193 
 TYR   0.009   0.001   TYR F 102 
 ARG   0.006   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04376 (  364)
  hydrogen bonds       : angle       3.76384 ( 1013)
  covalent geometry    : bond        0.00293 ( 7573)
  covalent geometry    : angle       0.50938 (10446)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.759 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 82
  average time/residue: 0.2805
  time to fit residues: 28.7134
Evaluate side-chains
  80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain B residue  152 LYS
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain F residue   88 ASP
Chi-restraints excluded: chain F residue   92 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0470
   chunk 35 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0040
   chunk 12 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.5290

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

Flipped N/Q/H residues before XYZ refinement:
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.103732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.075289 restraints weight = 34029.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 4.86
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3040
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3040
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7573  Z= 0.115
  Angle     :  0.496   6.752  10446  Z= 0.255
  Chirality :  0.035   0.156   1174
  Planarity :  0.004   0.043   1203
  Dihedral  : 19.025  79.854   1458
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 10.69 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.30), residues: 818
  helix:  2.71 (0.27), residues: 370
  sheet:  1.81 (0.43), residues: 148
  loop : -1.16 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 105 
 HIS   0.004   0.001   HIS A 277 
 PHE   0.008   0.001   PHE D  34 
 TYR   0.006   0.001   TYR B  79 
 ARG   0.005   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  364)
  hydrogen bonds       : angle       3.69131 ( 1013)
  covalent geometry    : bond        0.00259 ( 7573)
  covalent geometry    : angle       0.49626 (10446)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.767 
Fit side-chains
REVERT: A   97 LYS cc_start: 0.7818 (ptmm) cc_final: 0.7418 (ttmt)
REVERT: A  102 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7584 (mtm-85)
  outliers start: 7
  outliers final: 5
  residues processed: 81
  average time/residue: 0.2919
  time to fit residues: 29.3775
Evaluate side-chains
  80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain D residue    6 SER
Chi-restraints excluded: chain F residue   88 ASP
Chi-restraints excluded: chain F residue  163 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0670
   chunk 23 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0370
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.104790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.076624 restraints weight = 29960.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 4.59
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3064
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3064 r_free = 0.3064    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7573  Z= 0.107
  Angle     :  0.477   6.514  10446  Z= 0.246
  Chirality :  0.035   0.153   1174
  Planarity :  0.004   0.043   1203
  Dihedral  : 18.933  77.350   1458
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 10.21 %
    Favored  : 87.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.30), residues: 818
  helix:  2.76 (0.27), residues: 371
  sheet:  1.72 (0.42), residues: 153
  loop : -1.08 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 105 
 HIS   0.003   0.001   HIS A 277 
 PHE   0.008   0.001   PHE D  34 
 TYR   0.010   0.001   TYR F 102 
 ARG   0.006   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03681 (  364)
  hydrogen bonds       : angle       3.60244 ( 1013)
  covalent geometry    : bond        0.00240 ( 7573)
  covalent geometry    : angle       0.47669 (10446)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.772 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8038 (tm-30)
REVERT: A   97 LYS cc_start: 0.7792 (ptmm) cc_final: 0.7424 (ttmt)
REVERT: A  102 ARG cc_start: 0.7821 (mtm-85) cc_final: 0.7566 (mtm-85)
REVERT: B  173 ARG cc_start: 0.8289 (mtt90) cc_final: 0.7564 (mtm-85)
REVERT: D   16 ARG cc_start: 0.8222 (mtm110) cc_final: 0.7653 (ptm-80)
  outliers start: 13
  outliers final: 7
  residues processed: 85
  average time/residue: 0.2946
  time to fit residues: 31.0022
Evaluate side-chains
  83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain D residue    6 SER
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain F residue  139 THR
Chi-restraints excluded: chain F residue  163 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 76 optimal weight:    0.3980
   chunk 66 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.103021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.075475 restraints weight = 24969.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 4.15
r_work: 0.2853 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2854
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2854
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7573  Z= 0.132
  Angle     :  0.505   6.554  10446  Z= 0.260
  Chirality :  0.035   0.155   1174
  Planarity :  0.004   0.043   1203
  Dihedral  : 18.986  77.719   1458
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.48 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.30), residues: 818
  helix:  2.77 (0.27), residues: 371
  sheet:  1.68 (0.42), residues: 153
  loop : -1.14 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 105 
 HIS   0.005   0.001   HIS A 277 
 PHE   0.009   0.001   PHE A 193 
 TYR   0.006   0.001   TYR B  79 
 ARG   0.005   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04331 (  364)
  hydrogen bonds       : angle       3.65568 ( 1013)
  covalent geometry    : bond        0.00305 ( 7573)
  covalent geometry    : angle       0.50477 (10446)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8418 (tm-30)
REVERT: A   97 LYS cc_start: 0.8121 (ptmm) cc_final: 0.7766 (ttmt)
REVERT: B  173 ARG cc_start: 0.8555 (mtt90) cc_final: 0.8280 (mtt90)
REVERT: D   16 ARG cc_start: 0.8347 (mtm110) cc_final: 0.7749 (ptm-80)
  outliers start: 9
  outliers final: 6
  residues processed: 83
  average time/residue: 0.3040
  time to fit residues: 31.3606
Evaluate side-chains
  82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain D residue    6 SER
Chi-restraints excluded: chain F residue  139 THR
Chi-restraints excluded: chain F residue  163 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0060
   chunk 31 optimal weight:    0.7980
   chunk 75 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.103418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.075272 restraints weight = 27901.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 4.42
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3051
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3051 r_free = 0.3051    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3051 r_free = 0.3051    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3051
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7573  Z= 0.115
  Angle     :  0.493   6.482  10446  Z= 0.254
  Chirality :  0.035   0.157   1174
  Planarity :  0.004   0.043   1203
  Dihedral  : 18.965  76.623   1458
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 11.48 %
    Favored  : 86.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.30), residues: 818
  helix:  2.79 (0.27), residues: 371
  sheet:  1.68 (0.42), residues: 153
  loop : -1.10 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 105 
 HIS   0.004   0.001   HIS A 277 
 PHE   0.007   0.001   PHE D  34 
 TYR   0.011   0.001   TYR F 102 
 ARG   0.005   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03988 (  364)
  hydrogen bonds       : angle       3.61795 ( 1013)
  covalent geometry    : bond        0.00262 ( 7573)
  covalent geometry    : angle       0.49340 (10446)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.721 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8051 (tm-30)
REVERT: A   97 LYS cc_start: 0.7823 (ptmm) cc_final: 0.7463 (ttmt)
REVERT: B  173 ARG cc_start: 0.8289 (mtt90) cc_final: 0.7572 (mtm-85)
REVERT: D   16 ARG cc_start: 0.8288 (mtm110) cc_final: 0.7722 (ptm-80)
  outliers start: 10
  outliers final: 6
  residues processed: 83
  average time/residue: 0.3140
  time to fit residues: 32.1371
Evaluate side-chains
  82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain D residue    6 SER
Chi-restraints excluded: chain F residue  139 THR
Chi-restraints excluded: chain F residue  163 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 70 optimal weight:    0.0670
   chunk 76 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 69 optimal weight:    0.2980
   chunk 11 optimal weight:    0.0970
   overall best weight:    0.4516

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

Flipped N/Q/H residues before XYZ refinement:
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.103973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.075534 restraints weight = 30394.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 4.64
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3058
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3058
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7573  Z= 0.109
  Angle     :  0.490   6.673  10446  Z= 0.252
  Chirality :  0.035   0.158   1174
  Planarity :  0.004   0.046   1203
  Dihedral  : 18.914  74.024   1458
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.64 %
    Favored  : 86.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.30), residues: 818
  helix:  2.81 (0.27), residues: 371
  sheet:  1.66 (0.41), residues: 153
  loop : -1.06 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 105 
 HIS   0.003   0.001   HIS A 277 
 PHE   0.007   0.001   PHE D  34 
 TYR   0.006   0.001   TYR B  79 
 ARG   0.005   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03696 (  364)
  hydrogen bonds       : angle       3.56562 ( 1013)
  covalent geometry    : bond        0.00246 ( 7573)
  covalent geometry    : angle       0.48989 (10446)

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

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

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1636 Ramachandran restraints generated.
    818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.827 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7904 (tm-30)
REVERT: A   97 LYS cc_start: 0.7787 (ptmm) cc_final: 0.7436 (ttmt)
REVERT: D   16 ARG cc_start: 0.8354 (mtm110) cc_final: 0.7812 (ptm-80)
  outliers start: 9
  outliers final: 7
  residues processed: 80
  average time/residue: 0.2955
  time to fit residues: 29.4439
Evaluate side-chains
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain D residue    6 SER
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain F residue  139 THR
Chi-restraints excluded: chain F residue  163 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 55 optimal weight:    0.4980
   chunk 67 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0570
   chunk 68 optimal weight:    5.9990
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.103137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.075479 restraints weight = 23219.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 4.03
r_work: 0.2870 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2873
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2873 r_free = 0.2873    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2873
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7573  Z= 0.121
  Angle     :  0.494   6.585  10446  Z= 0.255
  Chirality :  0.035   0.155   1174
  Planarity :  0.004   0.045   1203
  Dihedral  : 18.921  73.744   1458
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.64 %
    Favored  : 86.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.30), residues: 818
  helix:  2.82 (0.27), residues: 371
  sheet:  1.67 (0.41), residues: 153
  loop : -1.10 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 105 
 HIS   0.004   0.001   HIS A 277 
 PHE   0.008   0.001   PHE A 193 
 TYR   0.010   0.001   TYR F 102 
 ARG   0.005   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04027 (  364)
  hydrogen bonds       : angle       3.60167 ( 1013)
  covalent geometry    : bond        0.00276 ( 7573)
  covalent geometry    : angle       0.49384 (10446)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3758.78 seconds
wall clock time: 65 minutes 37.80 seconds (3937.80 seconds total)