Starting phenix.real_space_refine
on Wed Sep 17 09:03:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8a93_15267/09_2025/8a93_15267.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a93_15267/09_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_15267/09_2025/8a93_15267.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a93_15267/09_2025/8a93_15267.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a93_15267/09_2025/8a93_15267.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a93_15267/09_2025/8a93_15267.cif"
  }
  resolution = 3.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 3.07, per 1000 atoms: 0.42
  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: 0.76
  Conformation dependent library (CDL) restraints added in 573.2 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.82
  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: 1.28

  Time building geometry restraints manager: 0.85 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 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 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:             4.380
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.550
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.620
-------------------------------------------------------------------------------
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 : 4.09
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  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
 ARG   0.008   0.000   ARG D  16 
 TYR   0.004   0.001   TYR B 178 
 PHE   0.008   0.001   PHE D  34 
 TRP   0.006   0.001   TRP A 105 
 HIS   0.003   0.001   HIS A 277 

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

*********************** 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  : 0.289 
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: 0.1350
  time to fit residues: 14.3965
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  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3522 r_free = 0.3522 target = 0.101934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.074209 restraints weight = 26514.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 4.26
r_work: 0.2830 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2833
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2833 r_free = 0.2833    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2833 r_free = 0.2833    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2833
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.1012

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= 0.152
  Angle     :  0.571   7.453  10446  Z= 0.297
  Chirality :  0.038   0.144   1174
  Planarity :  0.004   0.041   1203
  Dihedral  : 19.754  87.938   1458
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  6.70 %
    Favored  : 92.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.30), residues: 818
  helix:  2.49 (0.28), residues: 369
  sheet:  1.35 (0.43), residues: 148
  loop : -1.30 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 162 
 TYR   0.008   0.001   TYR B  79 
 PHE   0.010   0.001   PHE D  34 
 TRP   0.008   0.001   TRP B 105 
 HIS   0.006   0.001   HIS A 277 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 7573)
  covalent geometry    : angle       0.57136 (10446)
  hydrogen bonds       : bond        0.05210 (  364)
  hydrogen bonds       : angle       4.23310 ( 1013)

*********************** 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: 3
    poor density    : 76
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A   97 LYS cc_start: 0.8141 (ptmm) cc_final: 0.7738 (ptpp)
REVERT: A  102 ARG cc_start: 0.8539 (mtm-85) cc_final: 0.8261 (mtm-85)
REVERT: B  173 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.8225 (mtt90)
  outliers start: 3
  outliers final: 1
  residues processed: 79
  average time/residue: 0.1470
  time to fit residues: 14.2058
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  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 76 optimal weight:    0.0570
   chunk 58 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.5898

-------------------------------------------------------------------------------
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 = 0.3534 r_free = 0.3534 target = 0.102660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.073917 restraints weight = 39442.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 5.18
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3018
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3018 r_free = 0.3018    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3018 r_free = 0.3018    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3018
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1174

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= 0.125
  Angle     :  0.509   6.490  10446  Z= 0.265
  Chirality :  0.036   0.154   1174
  Planarity :  0.004   0.045   1203
  Dihedral  : 19.385  89.110   1458
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  8.93 %
    Favored  : 90.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.30), residues: 818
  helix:  2.54 (0.27), residues: 370
  sheet:  1.63 (0.43), residues: 148
  loop : -1.31 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  16 
 TYR   0.006   0.001   TYR B  79 
 PHE   0.009   0.001   PHE D  34 
 TRP   0.005   0.001   TRP B 105 
 HIS   0.004   0.001   HIS A 277 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 7573)
  covalent geometry    : angle       0.50883 (10446)
  hydrogen bonds       : bond        0.04634 (  364)
  hydrogen bonds       : angle       3.96506 ( 1013)

*********************** 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
  80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A   97 LYS cc_start: 0.7888 (ptmm) cc_final: 0.7564 (ptpp)
REVERT: A  102 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7685 (mtm-85)
  outliers start: 3
  outliers final: 2
  residues processed: 80
  average time/residue: 0.1538
  time to fit residues: 14.9809
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  : 0.273 
-------------------------------------------------------------------------------
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 9 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0010
   chunk 10 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0050
   chunk 39 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.4800

-------------------------------------------------------------------------------
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 = 0.3548 r_free = 0.3548 target = 0.103705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.076444 restraints weight = 23079.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 3.99
r_work: 0.2876 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2880
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    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 = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2880
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
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   0.031   7573  Z= 0.116
  Angle     :  0.505   6.535  10446  Z= 0.259
  Chirality :  0.036   0.127   1174
  Planarity :  0.004   0.046   1203
  Dihedral  : 19.155  84.396   1458
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.72 (0.30), residues: 818
  helix:  2.63 (0.27), residues: 370
  sheet:  1.76 (0.43), residues: 148
  loop : -1.23 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  16 
 TYR   0.006   0.001   TYR B  79 
 PHE   0.008   0.001   PHE D  34 
 TRP   0.005   0.001   TRP B 105 
 HIS   0.003   0.001   HIS A 277 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7573)
  covalent geometry    : angle       0.50476 (10446)
  hydrogen bonds       : bond        0.04130 (  364)
  hydrogen bonds       : angle       3.81294 ( 1013)

*********************** 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  : 0.263 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 81
  average time/residue: 0.1426
  time to fit residues: 14.2430
Evaluate side-chains
  78 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
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 48 optimal weight:    0.7980
   chunk 64 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 18 optimal weight:    0.4980
   chunk 11 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3534 r_free = 0.3534 target = 0.102928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.074363 restraints weight = 33191.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 4.79
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 = 0.37   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 = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3025
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7573  Z= 0.131
  Angle     :  0.506   6.808  10446  Z= 0.262
  Chirality :  0.036   0.149   1174
  Planarity :  0.004   0.044   1203
  Dihedral  : 19.082  82.025   1458
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.30), residues: 818
  helix:  2.66 (0.27), residues: 370
  sheet:  1.76 (0.43), residues: 148
  loop : -1.21 (0.34), residues: 300

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7573)
  covalent geometry    : angle       0.50636 (10446)
  hydrogen bonds       : bond        0.04476 (  364)
  hydrogen bonds       : angle       3.78443 ( 1013)

*********************** 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  : 0.301 
Fit side-chains
REVERT: A   97 LYS cc_start: 0.7936 (ptmm) cc_final: 0.7578 (ptpp)
  outliers start: 8
  outliers final: 5
  residues processed: 82
  average time/residue: 0.1481
  time to fit residues: 14.9377
Evaluate side-chains
  79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
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 82 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0270
   chunk 31 optimal weight:    0.6980
   chunk 76 optimal weight:    0.4980
   chunk 10 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0060
   chunk 44 optimal weight:    0.0060
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.2470

-------------------------------------------------------------------------------
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 = 0.3573 r_free = 0.3573 target = 0.105437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.077331 restraints weight = 30676.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 4.66
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7573  Z= 0.102
  Angle     :  0.488   6.934  10446  Z= 0.249
  Chirality :  0.035   0.153   1174
  Planarity :  0.004   0.042   1203
  Dihedral  : 18.958  77.394   1458
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 10.37 %
    Favored  : 88.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.31), residues: 818
  helix:  2.75 (0.27), residues: 371
  sheet:  1.72 (0.42), residues: 153
  loop : -1.04 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  16 
 TYR   0.005   0.001   TYR B 178 
 PHE   0.008   0.001   PHE D  34 
 TRP   0.009   0.001   TRP B 105 
 HIS   0.002   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 7573)
  covalent geometry    : angle       0.48785 (10446)
  hydrogen bonds       : bond        0.03334 (  364)
  hydrogen bonds       : angle       3.62202 ( 1013)

*********************** 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
  86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A   97 LYS cc_start: 0.7891 (ptmm) cc_final: 0.7535 (ptpp)
REVERT: B  173 ARG cc_start: 0.8266 (mtt90) cc_final: 0.7994 (mtm-85)
REVERT: C   46 LEU cc_start: 0.9130 (mt) cc_final: 0.8810 (mt)
  outliers start: 6
  outliers final: 5
  residues processed: 82
  average time/residue: 0.1549
  time to fit residues: 15.4306
Evaluate side-chains
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 43 optimal weight:    0.2980
   chunk 50 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 72 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.103144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.074483 restraints weight = 33750.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 4.83
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1506

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= 0.137
  Angle     :  0.512   6.730  10446  Z= 0.264
  Chirality :  0.036   0.152   1174
  Planarity :  0.004   0.043   1203
  Dihedral  : 19.023  79.237   1458
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.30), residues: 818
  helix:  2.74 (0.27), residues: 370
  sheet:  1.83 (0.42), residues: 148
  loop : -1.16 (0.35), residues: 300

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 7573)
  covalent geometry    : angle       0.51192 (10446)
  hydrogen bonds       : bond        0.04570 (  364)
  hydrogen bonds       : angle       3.69500 ( 1013)

*********************** 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
  85 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8056 (tm-30)
REVERT: A   97 LYS cc_start: 0.7915 (ptmm) cc_final: 0.7581 (ptpp)
REVERT: D   16 ARG cc_start: 0.8283 (mtm110) cc_final: 0.7650 (ptm-80)
  outliers start: 8
  outliers final: 5
  residues processed: 84
  average time/residue: 0.1478
  time to fit residues: 15.2239
Evaluate side-chains
  81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
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 C residue   49 ILE
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 18 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0070
   chunk 42 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 27 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0170
   chunk 55 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.4636

-------------------------------------------------------------------------------
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 = 0.3557 r_free = 0.3557 target = 0.104387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.075658 restraints weight = 36612.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 5.06
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3041
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3041 r_free = 0.3041    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 = 0.3041 r_free = 0.3041    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3041
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1575

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= 0.111
  Angle     :  0.498   6.967  10446  Z= 0.255
  Chirality :  0.035   0.155   1174
  Planarity :  0.004   0.043   1203
  Dihedral  : 18.969  77.669   1458
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.16 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.31), residues: 818
  helix:  2.79 (0.27), residues: 371
  sheet:  1.71 (0.42), residues: 153
  loop : -1.06 (0.36), residues: 294

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 7573)
  covalent geometry    : angle       0.49831 (10446)
  hydrogen bonds       : bond        0.03888 (  364)
  hydrogen bonds       : angle       3.62321 ( 1013)

*********************** 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  : 0.304 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8051 (tm-30)
REVERT: A   97 LYS cc_start: 0.7864 (ptmm) cc_final: 0.7530 (ptpp)
REVERT: B  173 ARG cc_start: 0.8273 (mtt90) cc_final: 0.7997 (mtm-85)
REVERT: D   16 ARG cc_start: 0.8272 (mtm110) cc_final: 0.7683 (ptm-80)
  outliers start: 9
  outliers final: 7
  residues processed: 81
  average time/residue: 0.1541
  time to fit residues: 15.2784
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  : 0.264 
-------------------------------------------------------------------------------
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   17 LEU
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 69 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0670
   chunk 14 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 60 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.6118

-------------------------------------------------------------------------------
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 = 0.103450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.075206 restraints weight = 29564.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 4.53
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1578

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= 0.122
  Angle     :  0.501   6.855  10446  Z= 0.257
  Chirality :  0.035   0.154   1174
  Planarity :  0.004   0.043   1203
  Dihedral  : 18.971  77.226   1458
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.48 %
    Favored  : 86.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.91 (0.31), residues: 818
  helix:  2.80 (0.27), residues: 371
  sheet:  1.71 (0.42), residues: 153
  loop : -1.11 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  16 
 TYR   0.006   0.001   TYR B  79 
 PHE   0.008   0.001   PHE A 193 
 TRP   0.008   0.001   TRP B 105 
 HIS   0.004   0.001   HIS A 277 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7573)
  covalent geometry    : angle       0.50083 (10446)
  hydrogen bonds       : bond        0.04127 (  364)
  hydrogen bonds       : angle       3.62802 ( 1013)

*********************** 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
  84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8051 (tm-30)
REVERT: A   97 LYS cc_start: 0.7881 (ptmm) cc_final: 0.7465 (ttmt)
REVERT: D   16 ARG cc_start: 0.8295 (mtm110) cc_final: 0.7717 (ptm-80)
  outliers start: 8
  outliers final: 6
  residues processed: 82
  average time/residue: 0.1455
  time to fit residues: 14.4370
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  : 0.238 
-------------------------------------------------------------------------------
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 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 21 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0040
   chunk 72 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0770
   chunk 78 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 5 optimal weight:    0.2980
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.3750

-------------------------------------------------------------------------------
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 = 0.3561 r_free = 0.3561 target = 0.104413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.075809 restraints weight = 31905.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 4.76
r_work (final): 0.3063
-------------------------------------------------------------------------------
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 = 0.40   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 = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1647

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= 0.106
  Angle     :  0.498   8.631  10446  Z= 0.254
  Chirality :  0.035   0.155   1174
  Planarity :  0.004   0.042   1203
  Dihedral  : 18.898  74.187   1458
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.31), residues: 818
  helix:  2.84 (0.27), residues: 371
  sheet:  1.76 (0.42), residues: 153
  loop : -1.03 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 173 
 TYR   0.011   0.001   TYR F 102 
 PHE   0.007   0.001   PHE D  34 
 TRP   0.009   0.001   TRP B 105 
 HIS   0.003   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 7573)
  covalent geometry    : angle       0.49844 (10446)
  hydrogen bonds       : bond        0.03551 (  364)
  hydrogen bonds       : angle       3.56162 ( 1013)

********************** 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  : 0.268 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8041 (tm-30)
REVERT: A   97 LYS cc_start: 0.7837 (ptmm) cc_final: 0.7511 (ptpp)
REVERT: D   16 ARG cc_start: 0.8354 (mtm110) cc_final: 0.7804 (ptm-80)
  outliers start: 9
  outliers final: 5
  residues processed: 80
  average time/residue: 0.1468
  time to fit residues: 14.4447
Evaluate side-chains
  79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
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  163 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0040
   chunk 24 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0270
   chunk 33 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.4650

-------------------------------------------------------------------------------
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 = 0.3558 r_free = 0.3558 target = 0.104027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.075560 restraints weight = 30318.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 4.63
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3059
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3059 r_free = 0.3059    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3059 r_free = 0.3059    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3059
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7573  Z= 0.111
  Angle     :  0.495   7.744  10446  Z= 0.253
  Chirality :  0.035   0.153   1174
  Planarity :  0.004   0.043   1203
  Dihedral  : 18.887  73.126   1458
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.64 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.31), residues: 818
  helix:  2.85 (0.27), residues: 371
  sheet:  1.79 (0.42), residues: 153
  loop : -1.03 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 173 
 TYR   0.005   0.001   TYR B  79 
 PHE   0.007   0.001   PHE D  34 
 TRP   0.009   0.001   TRP B 105 
 HIS   0.003   0.001   HIS A 277 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 7573)
  covalent geometry    : angle       0.49518 (10446)
  hydrogen bonds       : bond        0.03708 (  364)
  hydrogen bonds       : angle       3.56468 ( 1013)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1941.72 seconds
wall clock time: 33 minutes 51.64 seconds (2031.64 seconds total)