Starting phenix.real_space_refine
on Thu Jul  2 13:30:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uru_42501/07_2026/8uru_42501.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uru_42501/07_2026/8uru_42501.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uru_42501/07_2026/8uru_42501.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uru_42501/07_2026/8uru_42501.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uru_42501/07_2026/8uru_42501.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uru_42501/07_2026/8uru_42501.map"
  }
  resolution = 3.7
  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=   0.002 sd=   0.083
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      43      5.49       5
     Mg      1      5.21       5
     S      37      5.16       5
     C    5555      2.51       5
     N    1517      2.21       5
     O    1742      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8895
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2913
          Classifications: {'peptide': 363}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 347}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 1860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1860
          Classifications: {'peptide': 227}
          Link IDs: {'PTRANS': 12, 'TRANS': 214}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 2822
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 360, 2822
          Classifications: {'peptide': 360}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 350}
          Chain breaks: 6
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "F"
      Number of atoms: 417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 417
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 50}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "D"
      Number of atoms: 882
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 882
          Classifications: {'DNA': 43}
          Link IDs: {'rna3p': 42}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.14, per 1000 atoms: 0.24
  Number of scatterers: 8895
  At special positions: 0
  Unit cell: (110.656, 111.72, 118.104, 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      37     16.00
     P      43     15.00
     Mg      1     11.99
     O    1742      8.00
     N    1517      7.00
     C    5555      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: 0.73
  Conformation dependent library (CDL) restraints added in 487.2 milliseconds
  

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1920

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 14 sheets defined
      28.5% alpha, 12.8% beta
      17 base pairs and 34 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 21
    Processing helix  chain 'A' and resid 41 through 62
      removed outlier: 3.651A  pdb=" N   SER A  59 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU A  60 " --> pdb=" O   ALA A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 122
    Processing helix  chain 'A' and resid 130 through 137
      removed outlier: 3.623A  pdb=" N   ASN A 137 " --> pdb=" O   ILE A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 142
      removed outlier: 3.691A  pdb=" N   PHE A 141 " --> pdb=" O   ASN A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 158
      removed outlier: 4.044A  pdb=" N   VAL A 147 " --> pdb=" O   ARG A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 245
      removed outlier: 5.288A  pdb=" N   ASN A 243 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 276
    Processing helix  chain 'A' and resid 290 through 302
    Processing helix  chain 'A' and resid 320 through 328
      removed outlier: 6.174A  pdb=" N   LEU A 325 " --> pdb=" O   THR A 322 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   ALA A 326 " --> pdb=" O   GLN A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 355
    Processing helix  chain 'A' and resid 368 through 382
    Processing helix  chain 'B' and resid 75 through 87
      removed outlier: 3.607A  pdb=" N   LYS B  79 " --> pdb=" O   GLU B  75 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   GLU B  82 " --> pdb=" O   THR B  78 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   SER B  87 " --> pdb=" O   ILE B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 93
    Processing helix  chain 'B' and resid 119 through 127
    Processing helix  chain 'B' and resid 129 through 134
      removed outlier: 4.393A  pdb=" N   LEU B 133 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   HIS B 134 " --> pdb=" O   PRO B 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 129 through 134'
    Processing helix  chain 'B' and resid 167 through 183
      removed outlier: 3.968A  pdb=" N   TYR B 175 " --> pdb=" O   HIS B 171 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   PHE B 176 " --> pdb=" O   PHE B 172 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLN B 183 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 193
    Processing helix  chain 'B' and resid 196 through 204
    Processing helix  chain 'B' and resid 206 through 213
      removed outlier: 3.930A  pdb=" N   ILE B 210 " --> pdb=" O   SER B 206 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   SER B 211 " --> pdb=" O   LEU B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 229
      removed outlier: 3.848A  pdb=" N   ALA B 229 " --> pdb=" O   LEU B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 242
      removed outlier: 3.588A  pdb=" N   LEU B 241 " --> pdb=" O   ALA B 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 336
      removed outlier: 3.576A  pdb=" N   ASP C 335 " --> pdb=" O   HIS C 332 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 338 through 342
    Processing helix  chain 'F' and resid 13 through 21
      removed outlier: 3.662A  pdb=" N   LEU F  18 " --> pdb=" O   THR F  14 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   HIS F  19 " --> pdb=" O   GLN F  15 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   GLN F  20 " --> pdb=" O   ASP F  16 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   TYR F  21 " --> pdb=" O   PHE F  17 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 26 through 32
      removed outlier: 4.145A  pdb=" N   GLN F  30 " --> pdb=" O   ARG F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 42 through 58
      removed outlier: 3.545A  pdb=" N   THR F  57 " --> pdb=" O   ILE F  53 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ASN F  58 " --> pdb=" O   MET F  54 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28
      removed outlier: 6.953A  pdb=" N   ARG A  25 " --> pdb=" O   SER A  68 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   VAL A  70 " --> pdb=" O   ARG A  25 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ILE A  27 " --> pdb=" O   VAL A  70 " (cutoff:3.500A)
      removed outlier: 8.608A  pdb=" N   GLN A  72 " --> pdb=" O   ILE A  27 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 129
      removed outlier: 6.409A  pdb=" N   THR A 128 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176
    Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 185
    Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 285
    Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 5
      removed outlier: 4.337A  pdb=" N   ARG B  35 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ILE B  49 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
      removed outlier: 8.901A  pdb=" N   GLU B 148 " --> pdb=" O   ILE B  49 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 59
    Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11
      removed outlier: 4.037A  pdb=" N   ASP C 359 " --> pdb=" O   VAL C 382 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 41
      removed outlier: 3.512A  pdb=" N   LEU C  38 " --> pdb=" O   HIS C  58 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   VAL C  40 " --> pdb=" O   TYR C  56 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   TYR C  56 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 68 through 72
      removed outlier: 3.557A  pdb=" N   LEU C  83 " --> pdb=" O   LEU C  71 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   CYS C  82 " --> pdb=" O   ILE C  98 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   THR C  99 " --> pdb=" O   ILE C 108 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 124 through 130
      removed outlier: 3.742A  pdb=" N   ALA C 126 " --> pdb=" O   THR C 144 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LEU C 141 " --> pdb=" O   TRP C 153 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   TYR C 151 " --> pdb=" O   ALA C 143 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 199 through 202
      removed outlier: 3.510A  pdb=" N   ILE C 200 " --> pdb=" O   SER C 212 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLN C 210 " --> pdb=" O   THR C 202 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 250 through 254
      removed outlier: 3.507A  pdb=" N   CYS C 259 " --> pdb=" O   HIS C 252 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   ILE C 260 " --> pdb=" O   LEU C 274 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 294 through 296
      removed outlier: 6.682A  pdb=" N   ALA C 309 " --> pdb=" O   MET C 295 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ARG C 316 " --> pdb=" O   SER C 308 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLY C 310 " --> pdb=" O   LYS C 314 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   LYS C 314 " --> pdb=" O   GLY C 310 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   LEU C 315 " --> pdb=" O   THR C 328 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   THR C 328 " --> pdb=" O   LEU C 315 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   PHE C 317 " --> pdb=" O   ILE C 326 " (cutoff:3.500A)

    217 hydrogen bonds defined for protein.
    591 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      41 hydrogen bonds
      82 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      34 stacking parallelities
  Total time for adding SS restraints: 1.34

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1379
        1.32 -     1.44: 2675
        1.44 -     1.57: 4967
        1.57 -     1.70: 84
        1.70 -     1.83: 54
  Bond restraints: 9159
  Sorted by residual:
  bond pdb=" CA  PHE A  91 "
       pdb=" C   PHE A  91 "
    ideal  model  delta    sigma   weight residual
    1.525  1.483  0.042 1.07e-02 8.73e+03 1.51e+01
  bond pdb=" C   LEU A 175 "
       pdb=" O   LEU A 175 "
    ideal  model  delta    sigma   weight residual
    1.233  1.190  0.043 1.28e-02 6.10e+03 1.14e+01
  bond pdb=" C   PHE A  91 "
       pdb=" O   PHE A  91 "
    ideal  model  delta    sigma   weight residual
    1.245  1.198  0.047 1.53e-02 4.27e+03 9.58e+00
  bond pdb=" CA  ASP A  90 "
       pdb=" C   ASP A  90 "
    ideal  model  delta    sigma   weight residual
    1.526  1.485  0.041 1.37e-02 5.33e+03 8.95e+00
  bond pdb=" CA  LEU B 221 "
       pdb=" C   LEU B 221 "
    ideal  model  delta    sigma   weight residual
    1.524  1.488  0.036 1.26e-02 6.30e+03 7.94e+00
  ... (remaining 9154 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 12255
        2.68 -     5.37: 251
        5.37 -     8.05: 27
        8.05 -    10.74: 17
       10.74 -    13.42: 3
  Bond angle restraints: 12553
  Sorted by residual:
  angle pdb=" C   TYR B 188 "
        pdb=" N   PRO B 189 "
        pdb=" CA  PRO B 189 "
      ideal   model   delta    sigma   weight residual
     119.84  131.45  -11.61 1.25e+00 6.40e-01 8.62e+01
  angle pdb=" N   GLY A 174 "
        pdb=" CA  GLY A 174 "
        pdb=" C   GLY A 174 "
      ideal   model   delta    sigma   weight residual
     110.97  123.31  -12.34 1.56e+00 4.11e-01 6.26e+01
  angle pdb=" N   ALA A 171 "
        pdb=" CA  ALA A 171 "
        pdb=" C   ALA A 171 "
      ideal   model   delta    sigma   weight residual
     113.19  121.97   -8.78 1.19e+00 7.06e-01 5.44e+01
  angle pdb=" N   SER B 196 "
        pdb=" CA  SER B 196 "
        pdb=" C   SER B 196 "
      ideal   model   delta    sigma   weight residual
     112.93  104.56    8.37 1.33e+00 5.65e-01 3.96e+01
  angle pdb=" C   ILE A 353 "
        pdb=" CA  ILE A 353 "
        pdb=" CB  ILE A 353 "
      ideal   model   delta    sigma   weight residual
     111.06  105.69    5.37 8.80e-01 1.29e+00 3.72e+01
  ... (remaining 12548 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 4200
       17.88 -    35.76: 790
       35.76 -    53.64: 312
       53.64 -    71.51: 68
       71.51 -    89.39: 10
  Dihedral angle restraints: 5380
    sinusoidal: 2451
      harmonic: 2929
  Sorted by residual:
  dihedral pdb=" CA  SER B 218 "
           pdb=" C   SER B 218 "
           pdb=" N   VAL B 219 "
           pdb=" CA  VAL B 219 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.81  -27.19     0      5.00e+00 4.00e-02 2.96e+01
  dihedral pdb=" CA  MET A 253 "
           pdb=" C   MET A 253 "
           pdb=" N   LEU A 254 "
           pdb=" CA  LEU A 254 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.43  -23.57     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" N   GLN A 172 "
           pdb=" C   GLN A 172 "
           pdb=" CA  GLN A 172 "
           pdb=" CB  GLN A 172 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.33  -10.53     0      2.50e+00 1.60e-01 1.77e+01
  ... (remaining 5377 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 1316
       0.086 -    0.172: 100
       0.172 -    0.258: 13
       0.258 -    0.344: 2
       0.344 -    0.431: 2
  Chirality restraints: 1433
  Sorted by residual:
  chirality pdb=" CA  GLN A 172 "
            pdb=" N   GLN A 172 "
            pdb=" C   GLN A 172 "
            pdb=" CB  GLN A 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.63e+00
  chirality pdb=" CA  ALA A 171 "
            pdb=" N   ALA A 171 "
            pdb=" C   ALA A 171 "
            pdb=" CB  ALA A 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.14    0.34 2.00e-01 2.50e+01 2.97e+00
  chirality pdb=" CA  LEU B 221 "
            pdb=" N   LEU B 221 "
            pdb=" C   LEU B 221 "
            pdb=" CB  LEU B 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.94e+00
  ... (remaining 1430 not shown)

  Planarity restraints: 1426
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C  91 "   -0.015 2.00e-02 2.50e+03   2.96e-02 8.75e+00
        pdb=" C   GLY C  91 "    0.051 2.00e-02 2.50e+03
        pdb=" O   GLY C  91 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASP C  92 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 242 "   -0.045 5.00e-02 4.00e+02   6.82e-02 7.43e+00
        pdb=" N   PRO C 243 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO C 243 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO C 243 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  77 "    0.025 2.00e-02 2.50e+03   1.89e-02 6.28e+00
        pdb=" CG  PHE B  77 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  77 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  77 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  77 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  77 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  77 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1423 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 142
        2.63 -     3.19: 7855
        3.19 -     3.76: 13789
        3.76 -     4.33: 18078
        4.33 -     4.90: 28991
  Nonbonded interactions: 68855
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 288 "
            pdb="MG    MG A 501 "
     model   vdw
     2.058 2.170
  nonbonded pdb=" OD2 ASP A 290 "
            pdb="MG    MG A 501 "
     model   vdw
     2.122 2.170
  nonbonded pdb=" O   ILE B 165 "
            pdb=" OG  SER B 166 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" N   GLN F  30 "
            pdb=" OE1 GLN F  30 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" O   LYS A 173 "
            pdb=" NZ  LYS A 173 "
     model   vdw
     2.221 3.120
  ... (remaining 68850 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             1.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     10.230
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
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   0.064   9159  Z= 0.340
  Angle     :  0.998  13.421  12553  Z= 0.615
  Chirality :  0.052   0.431   1433
  Planarity :  0.006   0.068   1426
  Dihedral  : 21.437  89.392   3460
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 21.18
  Ramachandran Plot:
    Outliers :  0.94 %
    Allowed  : 10.95 %
    Favored  : 88.11 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 33.22 %
    Favored  : 63.57 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -2.97 (0.25), residues: 959
  helix: -0.16 (0.34), residues: 244
  sheet: -2.19 (0.37), residues: 176
  loop : -2.88 (0.23), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  13 
 TYR   0.014   0.001   TYR A 275 
 PHE   0.041   0.002   PHE B  77 
 TRP   0.025   0.002   TRP C  41 
 HIS   0.011   0.001   HIS C  15 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00505 /  0.34 ( 9159)
  covalent geometry    : angle       0.99812 /  0.62 (12553)
  hydrogen bonds       : bond        0.22871 / 15.28 (  258)
  hydrogen bonds       : angle       7.56729 /  5.64 (  673)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 144
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7707 (mtpt)
REVERT: A  378 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8039 (tm-30)
REVERT: B   47 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7633 (pp)
REVERT: B   82 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6861 (pt0)
REVERT: B  184 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8662 (tt)
REVERT: B  192 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7824 (m-80)
REVERT: B  221 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7131 (tt)
REVERT: C   53 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7110 (p0)
  outliers start: 29
  outliers final: 16
  residues processed: 165
  average time/residue: 0.0998
  time to fit residues: 22.5919
Evaluate side-chains
  143 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  101 HIS
Chi-restraints excluded: chain A residue  173 LYS
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain B residue   45 ASN
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  195 ILE
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  242 CYS
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   52 LYS
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  122 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.0770
   chunk 53 optimal weight:    0.1980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:   20.0000
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.6540

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  72 GLN
F  15 GLN
F  20 GLN
** F  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.183717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.141647 restraints weight = 12519.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.144347 restraints weight = 9754.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.145019 restraints weight = 7380.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.146012 restraints weight = 6592.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.146234 restraints weight = 6077.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.0970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   9159  Z= 0.154
  Angle     :  0.753   9.669  12553  Z= 0.390
  Chirality :  0.046   0.219   1433
  Planarity :  0.005   0.063   1426
  Dihedral  : 20.046  87.101   1569
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  :  9.91 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 28.90 %
    Favored  : 66.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -2.60 (0.26), residues: 959
  helix:  0.27 (0.33), residues: 246
  sheet: -2.12 (0.36), residues: 176
  loop : -2.66 (0.24), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 155 
 TYR   0.009   0.001   TYR A 177 
 PHE   0.019   0.002   PHE B  77 
 TRP   0.010   0.001   TRP C 129 
 HIS   0.008   0.001   HIS C  15 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.15 ( 9159)
  covalent geometry    : angle       0.75296 /  0.39 (12553)
  hydrogen bonds       : bond        0.05038 /  3.40 (  258)
  hydrogen bonds       : angle       5.83660 /  4.26 (  673)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 143
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7546 (pp)
REVERT: B   82 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6690 (pt0)
REVERT: B  128 SER cc_start: 0.7701 (OUTLIER) cc_final: 0.7485 (p)
REVERT: C   53 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7477 (p0)
REVERT: C  173 LEU cc_start: 0.7703 (tp) cc_final: 0.7392 (tp)
REVERT: C  229 MET cc_start: 0.4924 (ppp) cc_final: 0.4704 (ppp)
REVERT: F   25 GLU cc_start: 0.7779 (tp30) cc_final: 0.7538 (tp30)
  outliers start: 45
  outliers final: 26
  residues processed: 173
  average time/residue: 0.0901
  time to fit residues: 21.8670
Evaluate side-chains
  158 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  302 HIS
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   89 ARG
Chi-restraints excluded: chain B residue  128 SER
Chi-restraints excluded: chain B residue  190 MET
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain C residue   22 VAL
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   52 LYS
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  181 SER
Chi-restraints excluded: chain C residue  265 THR
Chi-restraints excluded: chain C residue  298 SER
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  382 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 102 optimal weight:   20.0000
   chunk 36 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 1 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  48 HIS
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 GLN
** B  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 250 GLN
** C  15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  15 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.182354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.139037 restraints weight = 12653.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.142202 restraints weight = 10378.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.142972 restraints weight = 7612.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.143292 restraints weight = 6634.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.143944 restraints weight = 6323.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.1350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9159  Z= 0.147
  Angle     :  0.712  11.112  12553  Z= 0.365
  Chirality :  0.045   0.250   1433
  Planarity :  0.005   0.058   1426
  Dihedral  : 19.809  86.233   1547
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  9.80 %
    Favored  : 89.68 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 29.01 %
    Favored  : 64.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -2.40 (0.26), residues: 959
  helix:  0.42 (0.34), residues: 245
  sheet: -1.95 (0.35), residues: 187
  loop : -2.54 (0.25), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 325 
 TYR   0.011   0.001   TYR A 275 
 PHE   0.016   0.002   PHE B  77 
 TRP   0.022   0.002   TRP C 318 
 HIS   0.006   0.001   HIS C  66 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.15 ( 9159)
  covalent geometry    : angle       0.71215 /  0.37 (12553)
  hydrogen bonds       : bond        0.04192 /  2.83 (  258)
  hydrogen bonds       : angle       5.48792 /  4.01 (  673)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 130
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7686 (ttp80)
REVERT: A  353 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8712 (tt)
REVERT: B   47 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7453 (pp)
REVERT: B   82 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6687 (pt0)
REVERT: C   53 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7557 (p0)
REVERT: C  173 LEU cc_start: 0.7787 (tp) cc_final: 0.7438 (tp)
REVERT: C  318 TRP cc_start: 0.7960 (m100) cc_final: 0.7715 (m100)
REVERT: C  362 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7741 (m-10)
REVERT: C  377 GLU cc_start: 0.6136 (OUTLIER) cc_final: 0.5665 (tt0)
REVERT: F   25 GLU cc_start: 0.7891 (tp30) cc_final: 0.7632 (tp30)
  outliers start: 55
  outliers final: 28
  residues processed: 172
  average time/residue: 0.0935
  time to fit residues: 22.2672
Evaluate side-chains
  157 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 124
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  208 CYS
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  302 HIS
Chi-restraints excluded: chain A residue  353 ILE
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   89 ARG
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  190 MET
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   52 LYS
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  181 SER
Chi-restraints excluded: chain C residue  261 THR
Chi-restraints excluded: chain C residue  296 SER
Chi-restraints excluded: chain C residue  298 SER
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain C residue  362 PHE
Chi-restraints excluded: chain C residue  377 GLU
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  382 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 94 optimal weight:    8.9990
   chunk 63 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   chunk 68 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9990
   chunk 89 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   chunk 37 optimal weight:    9.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  15 GLN
F  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.179078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.136322 restraints weight = 12899.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.137571 restraints weight = 10552.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.138842 restraints weight = 9446.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.139389 restraints weight = 7405.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.139839 restraints weight = 6913.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9159  Z= 0.184
  Angle     :  0.727   9.231  12553  Z= 0.373
  Chirality :  0.046   0.259   1433
  Planarity :  0.005   0.064   1426
  Dihedral  : 19.799  88.251   1542
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 10.95 %
    Favored  : 88.63 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 30.34 %
    Favored  : 63.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -2.45 (0.25), residues: 959
  helix:  0.31 (0.33), residues: 245
  sheet: -1.96 (0.37), residues: 175
  loop : -2.55 (0.24), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 244 
 TYR   0.018   0.002   TYR B 188 
 PHE   0.017   0.002   PHE C  59 
 TRP   0.010   0.001   TRP C 318 
 HIS   0.006   0.001   HIS C  66 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00419 /  0.18 ( 9159)
  covalent geometry    : angle       0.72666 /  0.37 (12553)
  hydrogen bonds       : bond        0.04072 /  2.75 (  258)
  hydrogen bonds       : angle       5.44972 /  3.98 (  673)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 127
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7671 (ttp80)
REVERT: A  339 LEU cc_start: 0.8295 (mt) cc_final: 0.7781 (mp)
REVERT: B   47 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7521 (pp)
REVERT: B   82 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6749 (pt0)
REVERT: C   53 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7738 (p0)
REVERT: C  362 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7920 (m-10)
REVERT: C  377 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5602 (tt0)
REVERT: F   25 GLU cc_start: 0.8059 (tp30) cc_final: 0.7713 (tp30)
  outliers start: 57
  outliers final: 36
  residues processed: 171
  average time/residue: 0.0958
  time to fit residues: 22.9137
Evaluate side-chains
  164 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 124
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  302 HIS
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   89 ARG
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  190 MET
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  195 ILE
Chi-restraints excluded: chain B residue  204 GLN
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   52 LYS
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue   68 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  181 SER
Chi-restraints excluded: chain C residue  183 MET
Chi-restraints excluded: chain C residue  261 THR
Chi-restraints excluded: chain C residue  296 SER
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain C residue  362 PHE
Chi-restraints excluded: chain C residue  377 GLU
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain F residue   35 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 93 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 94 optimal weight:    7.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    1.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 172 GLN
A 228 ASN
** B  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 ASN
** C  15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  35 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.178503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.135669 restraints weight = 12704.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.136202 restraints weight = 10310.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.137930 restraints weight = 9320.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.138361 restraints weight = 7425.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.138701 restraints weight = 7015.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9159  Z= 0.188
  Angle     :  0.721   9.295  12553  Z= 0.372
  Chirality :  0.045   0.273   1433
  Planarity :  0.005   0.063   1426
  Dihedral  : 19.747  87.121   1542
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 10.53 %
    Favored  : 89.05 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  : 30.01 %
    Favored  : 62.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -2.44 (0.26), residues: 959
  helix:  0.36 (0.33), residues: 245
  sheet: -1.93 (0.37), residues: 173
  loop : -2.56 (0.24), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 325 
 TYR   0.013   0.002   TYR A 177 
 PHE   0.015   0.002   PHE C  59 
 TRP   0.034   0.002   TRP C 318 
 HIS   0.006   0.001   HIS C  15 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00428 /  0.19 ( 9159)
  covalent geometry    : angle       0.72116 /  0.37 (12553)
  hydrogen bonds       : bond        0.04062 /  2.74 (  258)
  hydrogen bonds       : angle       5.43586 /  3.98 (  673)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 126
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 LEU cc_start: 0.8319 (mt) cc_final: 0.7792 (mp)
REVERT: B   47 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7560 (pp)
REVERT: B   82 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6774 (pt0)
REVERT: C   53 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7752 (p0)
REVERT: C  377 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.6042 (tt0)
REVERT: F   25 GLU cc_start: 0.8205 (tp30) cc_final: 0.7843 (tp30)
  outliers start: 65
  outliers final: 43
  residues processed: 175
  average time/residue: 0.0939
  time to fit residues: 22.9293
Evaluate side-chains
  168 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 122
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  302 HIS
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   89 ARG
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  190 MET
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  204 GLN
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain C residue   16 ASP
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   22 VAL
Chi-restraints excluded: chain C residue   37 TYR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   52 LYS
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue   68 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   71 LEU
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  122 HIS
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  181 SER
Chi-restraints excluded: chain C residue  183 MET
Chi-restraints excluded: chain C residue  296 SER
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain C residue  377 GLU
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain F residue   15 GLN
Chi-restraints excluded: chain F residue   35 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 89 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 101 optimal weight:   40.0000
   chunk 57 optimal weight:    3.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 228 ASN
** B  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 ASN
** C  15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  35 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.177247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.135535 restraints weight = 12684.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.136435 restraints weight = 10020.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.138121 restraints weight = 8657.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.139026 restraints weight = 7365.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.139753 restraints weight = 7083.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9159  Z= 0.199
  Angle     :  0.737  11.089  12553  Z= 0.379
  Chirality :  0.046   0.265   1433
  Planarity :  0.005   0.064   1426
  Dihedral  : 19.744  86.802   1542
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  : 11.68 %
    Favored  : 87.90 %
  Rotamer:
    Outliers :  7.75 %
    Allowed  : 30.01 %
    Favored  : 62.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -2.45 (0.25), residues: 959
  helix:  0.38 (0.33), residues: 246
  sheet: -2.01 (0.37), residues: 173
  loop : -2.57 (0.24), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  13 
 TYR   0.013   0.002   TYR A 177 
 PHE   0.020   0.002   PHE B  11 
 TRP   0.020   0.001   TRP C 318 
 HIS   0.005   0.001   HIS C  15 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00457 /  0.20 ( 9159)
  covalent geometry    : angle       0.73684 /  0.38 (12553)
  hydrogen bonds       : bond        0.04107 /  2.76 (  258)
  hydrogen bonds       : angle       5.45393 /  4.00 (  673)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 131
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 LEU cc_start: 0.8325 (mt) cc_final: 0.7796 (mp)
REVERT: B   47 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7534 (pp)
REVERT: B   82 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6730 (pt0)
REVERT: C   52 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.7026 (mmtm)
REVERT: C  318 TRP cc_start: 0.7877 (m100) cc_final: 0.6718 (m100)
REVERT: F   25 GLU cc_start: 0.8178 (tp30) cc_final: 0.7809 (tp30)
  outliers start: 70
  outliers final: 47
  residues processed: 183
  average time/residue: 0.0900
  time to fit residues: 23.2138
Evaluate side-chains
  172 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 123
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  302 HIS
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain B residue    6 THR
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   89 ARG
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  204 GLN
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain C residue   16 ASP
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   22 VAL
Chi-restraints excluded: chain C residue   37 TYR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   52 LYS
Chi-restraints excluded: chain C residue   68 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   71 LEU
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  122 HIS
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  181 SER
Chi-restraints excluded: chain C residue  183 MET
Chi-restraints excluded: chain C residue  194 ILE
Chi-restraints excluded: chain C residue  234 ASN
Chi-restraints excluded: chain C residue  259 CYS
Chi-restraints excluded: chain C residue  296 SER
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  350 ASP
Chi-restraints excluded: chain C residue  377 GLU
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   35 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 82 optimal weight:    0.0000
   chunk 2 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   chunk 47 optimal weight:    7.9990
   overall best weight:    0.6184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 228 ASN
** B  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 332 HIS
F  35 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.180819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.137916 restraints weight = 12807.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.138378 restraints weight = 10217.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.139728 restraints weight = 9447.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.140363 restraints weight = 7816.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.140659 restraints weight = 7347.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9159  Z= 0.136
  Angle     :  0.709  10.190  12553  Z= 0.363
  Chirality :  0.044   0.240   1433
  Planarity :  0.005   0.063   1426
  Dihedral  : 19.605  83.176   1540
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  9.38 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  6.64 %
    Allowed  : 30.56 %
    Favored  : 62.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -2.30 (0.26), residues: 959
  helix:  0.60 (0.34), residues: 246
  sheet: -2.08 (0.37), residues: 161
  loop : -2.47 (0.24), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 244 
 TYR   0.023   0.002   TYR A 275 
 PHE   0.012   0.001   PHE F  22 
 TRP   0.015   0.001   TRP C 318 
 HIS   0.007   0.001   HIS C 332 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.14 ( 9159)
  covalent geometry    : angle       0.70902 /  0.36 (12553)
  hydrogen bonds       : bond        0.03644 /  2.44 (  258)
  hydrogen bonds       : angle       5.30844 /  3.90 (  673)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 133
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 LEU cc_start: 0.7620 (mt) cc_final: 0.7279 (mt)
REVERT: A  220 LYS cc_start: 0.7818 (mmtt) cc_final: 0.7589 (mmtt)
REVERT: A  339 LEU cc_start: 0.8251 (mt) cc_final: 0.7746 (mp)
REVERT: B   47 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7515 (pp)
REVERT: B   82 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6812 (pt0)
REVERT: B  245 ARG cc_start: 0.7087 (mtm-85) cc_final: 0.6805 (ttp-110)
REVERT: C   52 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.7035 (mmtm)
REVERT: C  318 TRP cc_start: 0.7919 (m100) cc_final: 0.6813 (m100)
REVERT: F   25 GLU cc_start: 0.8177 (tp30) cc_final: 0.7818 (tp30)
  outliers start: 60
  outliers final: 39
  residues processed: 176
  average time/residue: 0.0929
  time to fit residues: 22.8950
Evaluate side-chains
  163 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 122
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  302 HIS
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   77 PHE
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  204 GLN
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain C residue   16 ASP
Chi-restraints excluded: chain C residue   37 TYR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   52 LYS
Chi-restraints excluded: chain C residue   66 HIS
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   71 LEU
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  122 HIS
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  181 SER
Chi-restraints excluded: chain C residue  183 MET
Chi-restraints excluded: chain C residue  194 ILE
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  234 ASN
Chi-restraints excluded: chain C residue  259 CYS
Chi-restraints excluded: chain C residue  296 SER
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  350 ASP
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain F residue   35 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 92 optimal weight:    0.1980
   chunk 14 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0030
   chunk 83 optimal weight:    0.3980
   chunk 68 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.6592

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 228 ASN
** B  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.180932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.139275 restraints weight = 12555.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.139679 restraints weight = 9742.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.141251 restraints weight = 9152.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.141651 restraints weight = 7467.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.142038 restraints weight = 7139.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   9159  Z= 0.138
  Angle     :  0.713   9.766  12553  Z= 0.362
  Chirality :  0.044   0.257   1433
  Planarity :  0.005   0.062   1426
  Dihedral  : 19.537  82.034   1538
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  :  9.59 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 32.45 %
    Favored  : 62.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -2.33 (0.26), residues: 959
  helix:  0.69 (0.34), residues: 246
  sheet: -2.43 (0.34), residues: 177
  loop : -2.40 (0.24), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 245 
 TYR   0.020   0.001   TYR A 275 
 PHE   0.022   0.001   PHE B  11 
 TRP   0.012   0.001   TRP C 318 
 HIS   0.004   0.001   HIS C  15 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.14 ( 9159)
  covalent geometry    : angle       0.71317 /  0.36 (12553)
  hydrogen bonds       : bond        0.03540 /  2.37 (  258)
  hydrogen bonds       : angle       5.26156 /  3.86 (  673)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 128
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 LEU cc_start: 0.8238 (mt) cc_final: 0.7739 (mp)
REVERT: B   82 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6835 (pt0)
REVERT: B  245 ARG cc_start: 0.7109 (mtm-85) cc_final: 0.6887 (ttp-110)
REVERT: C   52 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.7041 (mmtm)
REVERT: C  318 TRP cc_start: 0.7918 (m100) cc_final: 0.6926 (m100)
REVERT: F   16 ASP cc_start: 0.7647 (t0) cc_final: 0.7298 (t0)
  outliers start: 48
  outliers final: 37
  residues processed: 166
  average time/residue: 0.0867
  time to fit residues: 20.4464
Evaluate side-chains
  160 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 122
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  302 HIS
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  204 GLN
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain C residue   16 ASP
Chi-restraints excluded: chain C residue   37 TYR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   52 LYS
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   71 LEU
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  122 HIS
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  181 SER
Chi-restraints excluded: chain C residue  183 MET
Chi-restraints excluded: chain C residue  194 ILE
Chi-restraints excluded: chain C residue  234 ASN
Chi-restraints excluded: chain C residue  259 CYS
Chi-restraints excluded: chain C residue  296 SER
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain C residue  350 ASP
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   33 LEU
Chi-restraints excluded: chain F residue   35 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 228 ASN
** B  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 ASN
** C  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  34 ASN
F  35 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.180776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.138751 restraints weight = 12668.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.138814 restraints weight = 10069.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.139897 restraints weight = 9505.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.140806 restraints weight = 7871.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.141189 restraints weight = 7385.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9159  Z= 0.149
  Angle     :  0.720  11.822  12553  Z= 0.368
  Chirality :  0.044   0.277   1433
  Planarity :  0.005   0.084   1426
  Dihedral  : 19.501  81.540   1536
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  :  9.80 %
    Favored  : 89.57 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 31.89 %
    Favored  : 62.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -2.37 (0.26), residues: 959
  helix:  0.54 (0.34), residues: 250
  sheet: -2.44 (0.34), residues: 177
  loop : -2.39 (0.24), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 244 
 TYR   0.015   0.001   TYR A 275 
 PHE   0.019   0.001   PHE B  77 
 TRP   0.011   0.001   TRP C 318 
 HIS   0.004   0.001   HIS C  15 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.15 ( 9159)
  covalent geometry    : angle       0.71985 /  0.37 (12553)
  hydrogen bonds       : bond        0.03598 /  2.41 (  258)
  hydrogen bonds       : angle       5.27026 /  3.87 (  673)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 132
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 LYS cc_start: 0.7693 (mmtt) cc_final: 0.7476 (mmtt)
REVERT: A  339 LEU cc_start: 0.8249 (mt) cc_final: 0.7749 (mp)
REVERT: B   82 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6817 (pt0)
REVERT: B  245 ARG cc_start: 0.7062 (mtm-85) cc_final: 0.6828 (ttp-110)
REVERT: C   52 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.7070 (mmtm)
REVERT: C  318 TRP cc_start: 0.8036 (m100) cc_final: 0.7028 (m100)
REVERT: F   16 ASP cc_start: 0.7678 (t0) cc_final: 0.7332 (t0)
REVERT: F   25 GLU cc_start: 0.8145 (tp30) cc_final: 0.7750 (tp30)
  outliers start: 52
  outliers final: 39
  residues processed: 172
  average time/residue: 0.0785
  time to fit residues: 19.2120
Evaluate side-chains
  170 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 130
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  302 HIS
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  204 GLN
Chi-restraints excluded: chain B residue  217 ASN
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain C residue   16 ASP
Chi-restraints excluded: chain C residue   37 TYR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   52 LYS
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   71 LEU
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  122 HIS
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  181 SER
Chi-restraints excluded: chain C residue  183 MET
Chi-restraints excluded: chain C residue  194 ILE
Chi-restraints excluded: chain C residue  234 ASN
Chi-restraints excluded: chain C residue  259 CYS
Chi-restraints excluded: chain C residue  296 SER
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain C residue  311 TRP
Chi-restraints excluded: chain C residue  350 ASP
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   35 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 75 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   chunk 91 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 98 optimal weight:    8.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 228 ASN
** B  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.180627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.137697 restraints weight = 12683.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.137962 restraints weight = 10238.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.139345 restraints weight = 9459.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.139999 restraints weight = 7978.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.140226 restraints weight = 7417.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9159  Z= 0.153
  Angle     :  0.736  11.628  12553  Z= 0.375
  Chirality :  0.044   0.281   1433
  Planarity :  0.005   0.082   1426
  Dihedral  : 19.475  80.861   1536
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  : 10.01 %
    Favored  : 89.36 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 32.78 %
    Favored  : 62.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -2.35 (0.26), residues: 959
  helix:  0.65 (0.34), residues: 247
  sheet: -2.46 (0.34), residues: 178
  loop : -2.39 (0.24), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 244 
 TYR   0.016   0.001   TYR A 275 
 PHE   0.022   0.001   PHE B  11 
 TRP   0.011   0.001   TRP C 318 
 HIS   0.004   0.001   HIS C  15 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.15 ( 9159)
  covalent geometry    : angle       0.73566 /  0.38 (12553)
  hydrogen bonds       : bond        0.03633 /  2.44 (  258)
  hydrogen bonds       : angle       5.24027 /  3.85 (  673)

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 131
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 LEU cc_start: 0.8297 (mt) cc_final: 0.7762 (mp)
REVERT: B   47 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7524 (pp)
REVERT: B   82 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6798 (pt0)
REVERT: B  245 ARG cc_start: 0.7164 (mtm-85) cc_final: 0.6866 (ttp-110)
REVERT: C   52 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7069 (mmtm)
REVERT: C  318 TRP cc_start: 0.8058 (m100) cc_final: 0.7020 (m100)
REVERT: F   16 ASP cc_start: 0.7749 (t0) cc_final: 0.7383 (t0)
REVERT: F   25 GLU cc_start: 0.8162 (tp30) cc_final: 0.7807 (tp30)
  outliers start: 44
  outliers final: 38
  residues processed: 165
  average time/residue: 0.0781
  time to fit residues: 18.3546
Evaluate side-chains
  168 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 128
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  302 HIS
Chi-restraints excluded: chain A residue  309 TYR
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  187 GLU
Chi-restraints excluded: chain B residue  191 VAL
Chi-restraints excluded: chain B residue  204 GLN
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain C residue   37 TYR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   52 LYS
Chi-restraints excluded: chain C residue   66 HIS
Chi-restraints excluded: chain C residue   68 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   71 LEU
Chi-restraints excluded: chain C residue  114 LEU
Chi-restraints excluded: chain C residue  122 HIS
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  181 SER
Chi-restraints excluded: chain C residue  183 MET
Chi-restraints excluded: chain C residue  194 ILE
Chi-restraints excluded: chain C residue  234 ASN
Chi-restraints excluded: chain C residue  259 CYS
Chi-restraints excluded: chain C residue  296 SER
Chi-restraints excluded: chain C residue  305 THR
Chi-restraints excluded: chain C residue  350 ASP
Chi-restraints excluded: chain C residue  377 GLU
Chi-restraints excluded: chain C residue  379 LEU
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain F residue   18 LEU
Chi-restraints excluded: chain F residue   23 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 52 optimal weight:    0.1980
   chunk 49 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 76 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 228 ASN
** B  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 ASN
** C  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.181753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.138952 restraints weight = 12564.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.138629 restraints weight = 10067.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.139639 restraints weight = 9632.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.140620 restraints weight = 8178.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.140951 restraints weight = 7665.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9159  Z= 0.137
  Angle     :  0.715  11.312  12553  Z= 0.365
  Chirality :  0.044   0.281   1433
  Planarity :  0.005   0.082   1426
  Dihedral  : 19.407  78.429   1536
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  :  9.07 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 32.56 %
    Favored  : 62.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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: -2.21 (0.26), residues: 959
  helix:  0.86 (0.35), residues: 241
  sheet: -2.42 (0.34), residues: 178
  loop : -2.31 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 244 
 TYR   0.015   0.001   TYR B 188 
 PHE   0.017   0.001   PHE B  77 
 TRP   0.012   0.001   TRP C 318 
 HIS   0.005   0.001   HIS C  15 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.14 ( 9159)
  covalent geometry    : angle       0.71517 /  0.37 (12553)
  hydrogen bonds       : bond        0.03497 /  2.34 (  258)
  hydrogen bonds       : angle       5.23344 /  3.83 (  673)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1479.72 seconds
wall clock time: 26 minutes 24.83 seconds (1584.83 seconds total)