Starting phenix.real_space_refine
on Fri Jul 25 10:30:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8a93_15267/07_2025/8a93_15267.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a93_15267/07_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_15267/07_2025/8a93_15267.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a93_15267/07_2025/8a93_15267.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a93_15267/07_2025/8a93_15267.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a93_15267/07_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.65, per 1000 atoms: 1.18
  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: 2.21
  Conformation dependent library (CDL) restraints added in 1.4 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: 2.58
  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: 2.48

  Time building geometry restraints manager: 2.58 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:             3.200
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     27.680
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.620
-------------------------------------------------------------------------------
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  : 0.694 
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: 0.2760
  time to fit residues: 29.6318
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  : 0.688 
-------------------------------------------------------------------------------
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 = 0.101375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.073016 restraints weight = 31051.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 4.61
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3004
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    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 = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3004
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.1066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7573  Z= 0.173
  Angle     :  0.586   7.351  10446  Z= 0.305
  Chirality :  0.039   0.146   1174
  Planarity :  0.004   0.040   1203
  Dihedral  : 19.766  88.499   1458
  Min Nonbonded Distance : 1.943

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 244 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05473 (  364)
  hydrogen bonds       : angle       4.24781 ( 1013)
  covalent geometry    : bond        0.00400 ( 7573)
  covalent geometry    : angle       0.58594 (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  : 0.705 
Fit side-chains
REVERT: A  102 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7732 (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: 0.2973
  time to fit residues: 29.1244
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  : 0.708 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 66 optimal weight:    0.0870
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.6358

-------------------------------------------------------------------------------
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 = 0.3532 r_free = 0.3532 target = 0.102722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.075879 restraints weight = 19944.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 3.66
r_work: 0.2875 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2878
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    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 = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2878
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.1208

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= 0.128
  Angle     :  0.509   6.525  10446  Z= 0.266
  Chirality :  0.036   0.139   1174
  Planarity :  0.004   0.045   1203
  Dihedral  : 19.352  88.225   1458
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  8.93 %
    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:  1.55 (0.30), residues: 818
  helix:  2.53 (0.27), residues: 370
  sheet:  1.71 (0.43), residues: 146
  loop : -1.37 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 105 
 HIS   0.004   0.001   HIS A 277 
 PHE   0.010   0.001   PHE D  34 
 TYR   0.006   0.001   TYR B  79 
 ARG   0.002   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04667 (  364)
  hydrogen bonds       : angle       3.95413 ( 1013)
  covalent geometry    : bond        0.00286 ( 7573)
  covalent geometry    : angle       0.50893 (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
  79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.805 
Fit side-chains
REVERT: A   97 LYS cc_start: 0.8067 (ptmm) cc_final: 0.7675 (ptpp)
REVERT: A  102 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.8176 (mtm-85)
  outliers start: 4
  outliers final: 2
  residues processed: 79
  average time/residue: 0.3203
  time to fit residues: 31.3223
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  : 0.859 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 66 optimal weight:    0.4980
   chunk 74 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0370
   chunk 30 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.5258

-------------------------------------------------------------------------------
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 = 0.3541 r_free = 0.3541 target = 0.103471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.074668 restraints weight = 38273.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 5.11
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3027
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    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 = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3027
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7573  Z= 0.118
  Angle     :  0.502   6.384  10446  Z= 0.259
  Chirality :  0.036   0.127   1174
  Planarity :  0.004   0.046   1203
  Dihedral  : 19.156  84.539   1458
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  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:  1.67 (0.30), residues: 818
  helix:  2.61 (0.27), residues: 370
  sheet:  1.72 (0.43), residues: 148
  loop : -1.27 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  67 
 HIS   0.003   0.001   HIS A 277 
 PHE   0.008   0.001   PHE D  34 
 TYR   0.006   0.001   TYR B  79 
 ARG   0.004   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04247 (  364)
  hydrogen bonds       : angle       3.81736 ( 1013)
  covalent geometry    : bond        0.00263 ( 7573)
  covalent geometry    : angle       0.50197 (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
  82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.776 
Fit side-chains
  outliers start: 5
  outliers final: 1
  residues processed: 81
  average time/residue: 0.3009
  time to fit residues: 30.4090
Evaluate side-chains
  74 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   49 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0170
   chunk 30 optimal weight:    0.5980
   chunk 58 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0070
   chunk 50 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0980
   chunk 13 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.2836

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

Flipped N/Q/H residues before XYZ refinement:
A  69 HIS
B 284 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.105240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.077203 restraints weight = 30108.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 4.60
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3075
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3075
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7573  Z= 0.103
  Angle     :  0.480   6.000  10446  Z= 0.248
  Chirality :  0.035   0.156   1174
  Planarity :  0.004   0.043   1203
  Dihedral  : 18.989  78.233   1458
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  9.57 %
    Favored  : 88.68 %
  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:  2.68 (0.27), residues: 370
  sheet:  1.67 (0.43), residues: 153
  loop : -1.09 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 105 
 HIS   0.002   0.001   HIS A 257 
 PHE   0.008   0.001   PHE D  34 
 TYR   0.007   0.001   TYR F 102 
 ARG   0.006   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03531 (  364)
  hydrogen bonds       : angle       3.67098 ( 1013)
  covalent geometry    : bond        0.00225 ( 7573)
  covalent geometry    : angle       0.47980 (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
  87 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.895 
Fit side-chains
REVERT: A   97 LYS cc_start: 0.7802 (ptmm) cc_final: 0.7492 (ptpp)
REVERT: A  102 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.7679 (mtm-85)
  outliers start: 8
  outliers final: 5
  residues processed: 84
  average time/residue: 0.3141
  time to fit residues: 32.8213
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  : 0.830 
-------------------------------------------------------------------------------
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 D residue   17 LEU
Chi-restraints excluded: chain F residue   88 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.102841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.074106 restraints weight = 33668.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 4.84
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3025
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3025 r_free = 0.3025    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 = 0.3025 r_free = 0.3025    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3025
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7573  Z= 0.138
  Angle     :  0.509   5.906  10446  Z= 0.263
  Chirality :  0.036   0.154   1174
  Planarity :  0.004   0.043   1203
  Dihedral  : 19.021  79.419   1458
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 10.53 %
    Favored  : 87.88 %
  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:  1.79 (0.30), residues: 818
  helix:  2.69 (0.27), residues: 370
  sheet:  1.82 (0.43), residues: 148
  loop : -1.20 (0.35), residues: 300

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   0.010   0.001   PHE A 193 
 TYR   0.010   0.001   TYR F 102 
 ARG   0.003   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04472 (  364)
  hydrogen bonds       : angle       3.71555 ( 1013)
  covalent geometry    : bond        0.00320 ( 7573)
  covalent geometry    : angle       0.50855 (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
  85 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.812 
Fit side-chains
REVERT: A   97 LYS cc_start: 0.7809 (ptmm) cc_final: 0.7419 (ttmt)
REVERT: A  102 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7579 (mtm-85)
REVERT: B  173 ARG cc_start: 0.8313 (mtt90) cc_final: 0.7603 (mtm-85)
  outliers start: 7
  outliers final: 6
  residues processed: 82
  average time/residue: 0.3499
  time to fit residues: 36.3415
Evaluate side-chains
  83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain D residue   17 LEU
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:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0060
   overall best weight:    0.6196

-------------------------------------------------------------------------------
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 = 0.3544 r_free = 0.3544 target = 0.103406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.075311 restraints weight = 30002.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 4.55
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3042
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3042 r_free = 0.3042    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3042 r_free = 0.3042    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3042
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.1515

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= 0.122
  Angle     :  0.497   7.744  10446  Z= 0.257
  Chirality :  0.035   0.158   1174
  Planarity :  0.004   0.043   1203
  Dihedral  : 19.006  79.069   1458
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 10.69 %
    Favored  : 86.92 %
  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:  2.72 (0.27), residues: 370
  sheet:  1.66 (0.42), residues: 153
  loop : -1.14 (0.35), residues: 295

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   0.006   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04141 (  364)
  hydrogen bonds       : angle       3.66643 ( 1013)
  covalent geometry    : bond        0.00278 ( 7573)
  covalent geometry    : angle       0.49709 (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: 12
    poor density    : 78
  time to evaluate  : 0.882 
Fit side-chains
REVERT: A   97 LYS cc_start: 0.7802 (ptmm) cc_final: 0.7416 (ttmt)
REVERT: A  102 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7575 (mtm-85)
REVERT: B  173 ARG cc_start: 0.8301 (mtt90) cc_final: 0.7581 (mtm-85)
  outliers start: 12
  outliers final: 10
  residues processed: 85
  average time/residue: 0.3040
  time to fit residues: 32.1009
Evaluate side-chains
  87 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
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  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 D residue   24 THR
Chi-restraints excluded: chain F residue   88 ASP
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:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 82 optimal weight:    3.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.3519 r_free = 0.3519 target = 0.101950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.074275 restraints weight = 24113.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 4.07
r_work: 0.2836 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2840
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    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 = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7573  Z= 0.147
  Angle     :  0.521   6.852  10446  Z= 0.270
  Chirality :  0.036   0.158   1174
  Planarity :  0.004   0.043   1203
  Dihedral  : 19.075  80.651   1458
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.32 %
    Favored  : 86.28 %
  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:  1.75 (0.30), residues: 818
  helix:  2.69 (0.27), residues: 370
  sheet:  1.77 (0.42), residues: 148
  loop : -1.25 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 105 
 HIS   0.006   0.001   HIS A 277 
 PHE   0.010   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        0.04740 (  364)
  hydrogen bonds       : angle       3.73932 ( 1013)
  covalent geometry    : bond        0.00344 ( 7573)
  covalent geometry    : angle       0.52113 (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
  86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.774 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8408 (tm-30)
REVERT: A   97 LYS cc_start: 0.8079 (ptmm) cc_final: 0.7710 (ttmt)
REVERT: B  173 ARG cc_start: 0.8573 (mtt90) cc_final: 0.7942 (mtm-85)
  outliers start: 12
  outliers final: 8
  residues processed: 81
  average time/residue: 0.3086
  time to fit residues: 31.0094
Evaluate side-chains
  83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
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   24 THR
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:    0.0470
   chunk 38 optimal weight:    1.9990
   chunk 5 optimal weight:    0.1980
   chunk 31 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.5278

-------------------------------------------------------------------------------
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 = 0.3541 r_free = 0.3541 target = 0.102985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.074999 restraints weight = 27881.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 4.39
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3046
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    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 = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3046
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.1539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7573  Z= 0.117
  Angle     :  0.498   6.746  10446  Z= 0.257
  Chirality :  0.035   0.162   1174
  Planarity :  0.004   0.045   1203
  Dihedral  : 19.028  78.960   1458
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.32 %
    Favored  : 86.28 %
  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:  1.84 (0.30), residues: 818
  helix:  2.74 (0.27), residues: 371
  sheet:  1.67 (0.42), residues: 153
  loop : -1.14 (0.35), residues: 294

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   0.011   0.001   TYR F 102 
 ARG   0.007   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04046 (  364)
  hydrogen bonds       : angle       3.64109 ( 1013)
  covalent geometry    : bond        0.00265 ( 7573)
  covalent geometry    : angle       0.49825 (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: 12
    poor density    : 74
  time to evaluate  : 1.365 
Fit side-chains
REVERT: A   97 LYS cc_start: 0.7739 (ptmm) cc_final: 0.7371 (ttmt)
REVERT: A  102 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7588 (mtm-85)
REVERT: B  173 ARG cc_start: 0.8309 (mtt90) cc_final: 0.7606 (mtm-85)
REVERT: D   16 ARG cc_start: 0.8244 (mtm110) cc_final: 0.7719 (ptm-80)
  outliers start: 12
  outliers final: 10
  residues processed: 81
  average time/residue: 0.4026
  time to fit residues: 39.6874
Evaluate side-chains
  84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
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  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 D residue   24 THR
Chi-restraints excluded: chain F residue  136 VAL
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:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 18 optimal weight:    0.3980
   chunk 32 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0030
   overall best weight:    0.6592

-------------------------------------------------------------------------------
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 = 0.3536 r_free = 0.3536 target = 0.102931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.074578 restraints weight = 30395.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 4.60
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3033
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3033 r_free = 0.3033    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 = 0.3033 r_free = 0.3033    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3033
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.1586

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= 0.126
  Angle     :  0.505   8.255  10446  Z= 0.261
  Chirality :  0.035   0.159   1174
  Planarity :  0.004   0.046   1203
  Dihedral  : 19.020  78.319   1458
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.32 %
    Favored  : 86.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.30), residues: 818
  helix:  2.75 (0.27), residues: 371
  sheet:  1.66 (0.42), residues: 153
  loop : -1.17 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 105 
 HIS   0.005   0.001   HIS A 277 
 PHE   0.008   0.001   PHE A 193 
 TYR   0.006   0.001   TYR B  79 
 ARG   0.006   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04247 (  364)
  hydrogen bonds       : angle       3.64774 ( 1013)
  covalent geometry    : bond        0.00291 ( 7573)
  covalent geometry    : angle       0.50548 (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
  87 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.763 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7910 (tm-30)
REVERT: A   97 LYS cc_start: 0.7745 (ptmm) cc_final: 0.7380 (ttmt)
REVERT: A  102 ARG cc_start: 0.7855 (mtm-85) cc_final: 0.7562 (mtm-85)
REVERT: B  173 ARG cc_start: 0.8306 (mtt90) cc_final: 0.7603 (mtm-85)
REVERT: D   16 ARG cc_start: 0.8263 (mtm110) cc_final: 0.7721 (ptm-80)
  outliers start: 12
  outliers final: 10
  residues processed: 83
  average time/residue: 0.3088
  time to fit residues: 31.9260
Evaluate side-chains
  86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
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 D residue   24 THR
Chi-restraints excluded: chain F residue  136 VAL
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:    0.0970
   chunk 67 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3533 r_free = 0.3533 target = 0.102678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.075146 restraints weight = 22957.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 3.98
r_work: 0.2852 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    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 = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
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   0.035   7573  Z= 0.133
  Angle     :  0.512   7.651  10446  Z= 0.264
  Chirality :  0.036   0.158   1174
  Planarity :  0.004   0.046   1203
  Dihedral  : 19.033  78.065   1458
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.48 %
    Favored  : 86.12 %
  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:  1.81 (0.30), residues: 818
  helix:  2.74 (0.27), residues: 371
  sheet:  1.64 (0.42), residues: 153
  loop : -1.20 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   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   0.006   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04389 (  364)
  hydrogen bonds       : angle       3.66570 ( 1013)
  covalent geometry    : bond        0.00309 ( 7573)
  covalent geometry    : angle       0.51167 (10446)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4125.97 seconds
wall clock time: 71 minutes 56.48 seconds (4316.48 seconds total)