Starting phenix.real_space_refine
on Fri Sep 11 04:01:01 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8a93_15267/09_2026/8a93_15267.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8a93_15267/09_2026/8a93_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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8a93_15267/09_2026/8a93_15267.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8a93_15267/09_2026/8a93_15267.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8a93_15267/09_2026/8a93_15267.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8a93_15267/09_2026/8a93_15267.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8a93_15267/09_2026/8a93_15267.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8a93_15267/09_2026/8a93_15267.map"
  }
  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-2.2.1-6174/lib/python3.11/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: 2.49, per 1000 atoms: 0.34
  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: 0.64
  Conformation dependent library (CDL) restraints added in 512.9 milliseconds
  

  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: 0.73
  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: 1.23

  Time building geometry restraints manager: 0.72 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=" C3'  DT X  19 "
       pdb=" C2'  DT X  19 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.75e+00
  ... (remaining 7568 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 10291
        2.20 -     4.40: 133
        4.40 -     6.60: 15
        6.60 -     8.80: 5
        8.80 -    11.01: 2
  Bond angle restraints: 10446
  Sorted by residual:
  angle pdb=" N3   DT X  10 "
        pdb=" C4   DT X  10 "
        pdb=" O4   DT X  10 "
      ideal   model   delta    sigma   weight residual
     119.90  122.40   -2.50 6.00e-01 2.78e+00 1.74e+01
  angle pdb=" N3   DT X  19 "
        pdb=" C4   DT X  19 "
        pdb=" O4   DT X  19 "
      ideal   model   delta    sigma   weight residual
     119.90  122.39   -2.49 6.00e-01 2.78e+00 1.73e+01
  angle pdb=" N3   DT Y  19 "
        pdb=" C4   DT Y  19 "
        pdb=" O4   DT Y  19 "
      ideal   model   delta    sigma   weight residual
     119.90  122.35   -2.45 6.00e-01 2.78e+00 1.66e+01
  angle pdb=" N3   DT Y  21 "
        pdb=" C4   DT Y  21 "
        pdb=" O4   DT Y  21 "
      ideal   model   delta    sigma   weight residual
     119.90  122.34   -2.44 6.00e-01 2.78e+00 1.66e+01
  angle pdb=" N3   DT X   8 "
        pdb=" C4   DT X   8 "
        pdb=" O4   DT X   8 "
      ideal   model   delta    sigma   weight residual
     119.90  122.33   -2.43 6.00e-01 2.78e+00 1.63e+01
  ... (remaining 10441 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3729
       17.95 -    35.89: 447
       35.89 -    53.84: 231
       53.84 -    71.79: 21
       71.79 -    89.73: 4
  Dihedral angle restraints: 4432
    sinusoidal: 2083
      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 4429 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1014
       0.057 -    0.113: 154
       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:             4.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.580
  Find NCS groups from input model:        0.130
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
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= 0.325
  Angle     :  0.618  11.006  10446  Z= 0.370
  Chirality :  0.040   0.283   1174
  Planarity :  0.004   0.035   1203
  Dihedral  : 18.248  89.732   2926
  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 are 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/Z
  covalent geometry    : bond        0.00504 /  0.33 ( 7573)
  covalent geometry    : angle       0.61820 /  0.37 (10446)
  hydrogen bonds       : bond        0.21551 / 14.05 (  364)
  hydrogen bonds       : angle       5.98818 /  3.99 ( 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  : 0.253 
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: 0.1182
  time to fit residues: 12.7280
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  : 0.253 
-------------------------------------------------------------------------------
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...
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.102062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.074430 restraints weight = 26811.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 4.28
r_work: 0.2826 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2829
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2829
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.0839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7573  Z= 0.151
  Angle     :  0.584   6.773  10446  Z= 0.311
  Chirality :  0.040   0.171   1174
  Planarity :  0.004   0.044   1203
  Dihedral  : 19.158  67.489   1402
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  7.02 %
    Favored  : 92.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.31), residues: 818
  helix:  2.49 (0.28), residues: 370
  sheet:  1.39 (0.43), residues: 148
  loop : -1.30 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 162 
 TYR   0.006   0.001   TYR A  79 
 PHE   0.011   0.001   PHE D  34 
 TRP   0.005   0.001   TRP B 105 
 HIS   0.005   0.001   HIS A 277 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.15 ( 7573)
  covalent geometry    : angle       0.58374 /  0.31 (10446)
  hydrogen bonds       : bond        0.05894 /  4.03 (  364)
  hydrogen bonds       : angle       4.35190 /  2.94 ( 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
  76 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.342 
Fit side-chains
  outliers start: 3
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1373
  time to fit residues: 12.9847
Evaluate side-chains
  69 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 83 optimal weight:   10.0000
   chunk 55 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.102221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.073230 restraints weight = 38613.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 5.17
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3015
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    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 = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3015
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.1103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7573  Z= 0.125
  Angle     :  0.535   6.955  10446  Z= 0.280
  Chirality :  0.039   0.168   1174
  Planarity :  0.004   0.046   1203
  Dihedral  : 19.453  63.462   1402
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  :  8.45 %
    Favored  : 89.63 %
  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 are not related in a simple way.
  whole:  1.54 (0.30), residues: 818
  helix:  2.50 (0.27), residues: 370
  sheet:  1.60 (0.43), residues: 148
  loop : -1.30 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  16 
 TYR   0.011   0.001   TYR F 102 
 PHE   0.009   0.001   PHE D  34 
 TRP   0.006   0.001   TRP B 105 
 HIS   0.004   0.001   HIS A 277 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.13 ( 7573)
  covalent geometry    : angle       0.53456 /  0.28 (10446)
  hydrogen bonds       : bond        0.04955 /  3.44 (  364)
  hydrogen bonds       : angle       4.06901 /  2.74 ( 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
  84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.236 
Fit side-chains
REVERT: B  173 ARG cc_start: 0.8236 (mtm-85) cc_final: 0.7899 (mtt90)
REVERT: D   10 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9220 (tp)
  outliers start: 9
  outliers final: 4
  residues processed: 81
  average time/residue: 0.1353
  time to fit residues: 13.5359
Evaluate side-chains
  77 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
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  225 LEU
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain F residue   92 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 45 optimal weight:    0.2980
   chunk 5 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 71 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.102612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.075104 restraints weight = 23095.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 4.00
r_work: 0.2861 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7573  Z= 0.119
  Angle     :  0.521   6.785  10446  Z= 0.273
  Chirality :  0.038   0.136   1174
  Planarity :  0.004   0.046   1203
  Dihedral  : 19.411  61.246   1402
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  9.89 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.66 (0.30), residues: 818
  helix:  2.59 (0.27), residues: 370
  sheet:  1.70 (0.43), residues: 148
  loop : -1.25 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  16 
 TYR   0.007   0.001   TYR B  79 
 PHE   0.008   0.001   PHE D  34 
 TRP   0.006   0.001   TRP A  67 
 HIS   0.004   0.001   HIS A 277 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.12 ( 7573)
  covalent geometry    : angle       0.52135 /  0.27 (10446)
  hydrogen bonds       : bond        0.04556 /  3.16 (  364)
  hydrogen bonds       : angle       3.91831 /  2.64 ( 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
  83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.257 
Fit side-chains
REVERT: B  173 ARG cc_start: 0.8476 (mtm-85) cc_final: 0.8191 (mtt90)
REVERT: D   10 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9183 (tp)
  outliers start: 6
  outliers final: 4
  residues processed: 81
  average time/residue: 0.1325
  time to fit residues: 13.2538
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  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain F residue   92 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 1 optimal weight:    0.4980
   chunk 0 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0770
   chunk 9 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 84 optimal weight:    9.9990
   overall best weight:    0.6540

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.102429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.073827 restraints weight = 33235.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 4.81
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3026
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    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 = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3026
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.1313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7573  Z= 0.122
  Angle     :  0.514   6.284  10446  Z= 0.267
  Chirality :  0.037   0.123   1174
  Planarity :  0.004   0.045   1203
  Dihedral  : 19.411  59.355   1402
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 10.37 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.30), residues: 818
  helix:  2.62 (0.27), residues: 370
  sheet:  1.71 (0.43), residues: 148
  loop : -1.22 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  16 
 TYR   0.007   0.001   TYR B  79 
 PHE   0.008   0.001   PHE A 193 
 TRP   0.005   0.001   TRP B 105 
 HIS   0.004   0.001   HIS A 277 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 ( 7573)
  covalent geometry    : angle       0.51443 /  0.27 (10446)
  hydrogen bonds       : bond        0.04527 /  3.13 (  364)
  hydrogen bonds       : angle       3.83648 /  2.59 ( 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: 9
    poor density    : 76
  time to evaluate  : 0.261 
Fit side-chains
REVERT: D   10 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9128 (tp)
  outliers start: 9
  outliers final: 6
  residues processed: 83
  average time/residue: 0.1350
  time to fit residues: 13.9085
Evaluate side-chains
  80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
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  225 LEU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   24 THR
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:    9.9990
   chunk 77 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 76 optimal weight:    0.4980
   chunk 10 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0370
   chunk 44 optimal weight:    0.0670
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.4796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.103106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.074783 restraints weight = 30627.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 4.63
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3044
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3044 r_free = 0.3044    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 = 0.3044 r_free = 0.3044    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3044
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.1378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7573  Z= 0.110
  Angle     :  0.504   6.114  10446  Z= 0.261
  Chirality :  0.037   0.161   1174
  Planarity :  0.004   0.044   1203
  Dihedral  : 19.401  59.477   1402
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  :  9.89 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.30), residues: 818
  helix:  2.68 (0.27), residues: 370
  sheet:  1.76 (0.43), residues: 148
  loop : -1.17 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  16 
 TYR   0.008   0.001   TYR F 102 
 PHE   0.008   0.001   PHE D  34 
 TRP   0.008   0.001   TRP B 105 
 HIS   0.003   0.001   HIS A 277 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00229 /  0.11 ( 7573)
  covalent geometry    : angle       0.50358 /  0.26 (10446)
  hydrogen bonds       : bond        0.04219 /  2.92 (  364)
  hydrogen bonds       : angle       3.78269 /  2.55 ( 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: 11
    poor density    : 75
  time to evaluate  : 0.158 
Fit side-chains
REVERT: D   10 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9132 (tp)
  outliers start: 11
  outliers final: 7
  residues processed: 82
  average time/residue: 0.1334
  time to fit residues: 13.5505
Evaluate side-chains
  82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 GLU
Chi-restraints excluded: chain B residue  152 LYS
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain F residue   88 ASP
Chi-restraints excluded: chain F residue   92 LEU
Chi-restraints excluded: chain F residue  139 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 43 optimal weight:    0.2980
   chunk 50 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 81 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0970
   overall best weight:    0.5378

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.103250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.074581 restraints weight = 34110.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 4.86
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3039
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    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 = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3039
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.1442

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= 0.113
  Angle     :  0.516   8.446  10446  Z= 0.265
  Chirality :  0.037   0.188   1174
  Planarity :  0.004   0.044   1203
  Dihedral  : 19.405  59.789   1402
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 10.53 %
    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 are not related in a simple way.
  whole:  1.78 (0.30), residues: 818
  helix:  2.66 (0.27), residues: 371
  sheet:  1.62 (0.42), residues: 153
  loop : -1.12 (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   0.007   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/Z
  covalent geometry    : bond        0.00243 /  0.11 ( 7573)
  covalent geometry    : angle       0.51621 /  0.26 (10446)
  hydrogen bonds       : bond        0.04175 /  2.88 (  364)
  hydrogen bonds       : angle       3.76765 /  2.54 ( 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
  86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  102 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7623 (mtm-85)
REVERT: D   10 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9100 (tp)
REVERT: D   16 ARG cc_start: 0.8249 (mtm110) cc_final: 0.7574 (ptm-80)
  outliers start: 11
  outliers final: 8
  residues processed: 80
  average time/residue: 0.1300
  time to fit residues: 12.9468
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  : 0.253 
-------------------------------------------------------------------------------
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  152 LYS
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain F residue   92 LEU
Chi-restraints excluded: chain F residue  139 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 79 optimal weight:    0.8980
   chunk 35 optimal weight:    0.3980
   chunk 50 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.102907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.074022 restraints weight = 36189.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 5.00
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3016
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3016
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.1480

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= 0.133
  Angle     :  0.523   7.644  10446  Z= 0.270
  Chirality :  0.037   0.155   1174
  Planarity :  0.004   0.043   1203
  Dihedral  : 19.431  59.917   1402
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 11.32 %
    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 are not related in a simple way.
  whole:  1.72 (0.30), residues: 818
  helix:  2.66 (0.27), residues: 370
  sheet:  1.75 (0.42), residues: 148
  loop : -1.24 (0.34), residues: 300

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   0.010   0.001   PHE A 193 
 TRP   0.008   0.001   TRP B 105 
 HIS   0.005   0.001   HIS A 277 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.13 ( 7573)
  covalent geometry    : angle       0.52307 /  0.27 (10446)
  hydrogen bonds       : bond        0.04604 /  3.16 (  364)
  hydrogen bonds       : angle       3.79193 /  2.57 ( 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: 10
    poor density    : 74
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  102 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7606 (mtm-85)
REVERT: D   10 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9089 (tp)
  outliers start: 10
  outliers final: 7
  residues processed: 80
  average time/residue: 0.1315
  time to fit residues: 13.2497
Evaluate side-chains
  80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
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  152 LYS
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain F residue   92 LEU
Chi-restraints excluded: chain F residue  139 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 67 optimal weight:    3.9990
   chunk 19 optimal weight:    0.4980
   chunk 31 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.102712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.074400 restraints weight = 28375.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 4.46
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3035
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    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 = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3035
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.1480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7573  Z= 0.125
  Angle     :  0.522   7.635  10446  Z= 0.269
  Chirality :  0.037   0.159   1174
  Planarity :  0.004   0.044   1203
  Dihedral  : 19.426  59.945   1402
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.64 %
    Favored  : 86.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.30), residues: 818
  helix:  2.66 (0.27), residues: 370
  sheet:  1.78 (0.42), 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   0.009   0.001   TYR F 102 
 PHE   0.008   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/Z
  covalent geometry    : bond        0.00276 /  0.12 ( 7573)
  covalent geometry    : angle       0.52158 /  0.27 (10446)
  hydrogen bonds       : bond        0.04447 /  3.05 (  364)
  hydrogen bonds       : angle       3.76641 /  2.55 ( 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
  80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A   97 LYS cc_start: 0.7808 (ptmm) cc_final: 0.7426 (ttmt)
REVERT: A  102 ARG cc_start: 0.7945 (mtm-85) cc_final: 0.7581 (mtm-85)
REVERT: D   10 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9079 (tp)
  outliers start: 9
  outliers final: 7
  residues processed: 77
  average time/residue: 0.1224
  time to fit residues: 11.9094
Evaluate side-chains
  78 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
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  152 LYS
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain F residue   92 LEU
Chi-restraints excluded: chain F residue  139 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 82 optimal weight:    8.9990
   chunk 52 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0980
   chunk 78 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0370
   chunk 53 optimal weight:    0.4980
   overall best weight:    0.4058

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.103703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.075002 restraints weight = 31981.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 4.76
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.1551

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= 0.106
  Angle     :  0.507   7.974  10446  Z= 0.259
  Chirality :  0.036   0.160   1174
  Planarity :  0.004   0.046   1203
  Dihedral  : 19.391  59.858   1402
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.64 %
    Favored  : 86.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.30), residues: 818
  helix:  2.72 (0.27), residues: 370
  sheet:  1.68 (0.42), residues: 153
  loop : -1.12 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  16 
 TYR   0.006   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/Z
  covalent geometry    : bond        0.00222 /  0.11 ( 7573)
  covalent geometry    : angle       0.50658 /  0.26 (10446)
  hydrogen bonds       : bond        0.03907 /  2.68 (  364)
  hydrogen bonds       : angle       3.69194 /  2.49 ( 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
  85 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8076 (tm-30)
REVERT: A   97 LYS cc_start: 0.7837 (ptmm) cc_final: 0.7442 (ttmt)
REVERT: A  102 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7574 (mtm-85)
REVERT: D   10 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9054 (tp)
REVERT: D   16 ARG cc_start: 0.8272 (mtm110) cc_final: 0.7687 (ptm-80)
  outliers start: 9
  outliers final: 4
  residues processed: 80
  average time/residue: 0.1329
  time to fit residues: 13.2014
Evaluate side-chains
  80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
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  225 LEU
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain F residue   92 LEU
Chi-restraints excluded: chain F residue  139 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 69 optimal weight:    0.1980
   chunk 12 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0170
   chunk 5 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.6018

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.103775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.075473 restraints weight = 30384.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 4.61
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 = 0.40   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 = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.1544

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= 0.117
  Angle     :  0.512   7.954  10446  Z= 0.262
  Chirality :  0.036   0.159   1174
  Planarity :  0.004   0.046   1203
  Dihedral  : 19.397  59.970   1402
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 12.12 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.30), residues: 818
  helix:  2.71 (0.27), residues: 371
  sheet:  1.68 (0.42), residues: 153
  loop : -1.13 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 173 
 TYR   0.007   0.001   TYR F 102 
 PHE   0.008   0.001   PHE A 193 
 TRP   0.009   0.001   TRP B 105 
 HIS   0.004   0.001   HIS A 277 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.12 ( 7573)
  covalent geometry    : angle       0.51201 /  0.26 (10446)
  hydrogen bonds       : bond        0.04138 /  2.83 (  364)
  hydrogen bonds       : angle       3.68178 /  2.49 ( 1013)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1814.49 seconds
wall clock time: 31 minutes 45.27 seconds (1905.27 seconds total)