Starting phenix.real_space_refine
on Wed Feb 12 04:38:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iq6_35658/02_2025/8iq6_35658.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iq6_35658/02_2025/8iq6_35658.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iq6_35658/02_2025/8iq6_35658.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iq6_35658/02_2025/8iq6_35658.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iq6_35658/02_2025/8iq6_35658.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iq6_35658/02_2025/8iq6_35658.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.066
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: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    4541      2.51       5
     N    1203      2.21       5
     O    1263      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7059
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1560
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 3, 'TRANS': 197}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 115
          Unresolved non-hydrogen angles: 136
          Unresolved non-hydrogen dihedrals: 94
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 7, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 82
    Chain: "B"
      Number of atoms: 2342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2342
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 52}
          Link IDs: {'PTRANS': 5, 'TRANS': 323}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 187
          Unresolved non-hydrogen angles: 230
          Unresolved non-hydrogen dihedrals: 146
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 142
    Chain: "G"
      Number of atoms: 238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 238
          Classifications: {'peptide': 36}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 1, 'TRANS': 34}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "N"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 845
          Classifications: {'peptide': 114}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 109}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "R"
      Number of atoms: 2046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2046
          Classifications: {'peptide': 274}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 5, 'TRANS': 268}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 123
          Unresolved non-hydrogen angles: 153
          Unresolved non-hydrogen dihedrals: 104
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 77
    Chain: "R"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'7WT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.11, per 1000 atoms: 0.72
  Number of scatterers: 7059
  At special positions: 0
  Unit cell: (71.3635, 97.7131, 125.161, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1263      8.00
     N    1203      7.00
     C    4541      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 108 " - pdb=" SG  CYS R 186 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.85
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1794

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 11 sheets defined
      41.3% alpha, 21.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 38
      removed outlier: 3.616A  pdb=" N   GLU A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.583A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 293 through 302
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.511A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 352
      removed outlier: 3.782A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 392
    Processing helix  chain 'B' and resid 8 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 16 through 23
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.616A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'N' and resid 62 through 65
      removed outlier: 3.777A  pdb=" N   LYS N  65 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 62 through 65'
    Processing helix  chain 'R' and resid 29 through 59
      removed outlier: 4.367A  pdb=" N   SER R  33 " --> pdb=" O   SER R  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 62
      No H-bonds generated for 'chain 'R' and resid 60 through 62'
    Processing helix  chain 'R' and resid 64 through 94
    Processing helix  chain 'R' and resid 98 through 102
      removed outlier: 4.320A  pdb=" N   PHE R 101 " --> pdb=" O   TRP R  98 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ASP R 102 " --> pdb=" O   ILE R  99 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 98 through 102'
    Processing helix  chain 'R' and resid 105 through 139
      Proline residue:  R 122  - end of helix
    Processing helix  chain 'R' and resid 139 through 146
    Processing helix  chain 'R' and resid 147 through 173
      removed outlier: 4.143A  pdb=" N   HIS R 151 " --> pdb=" O   ILE R 147 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   VAL R 152 " --> pdb=" O   THR R 148 " (cutoff:3.500A)
      Proline residue:  R 170  - end of helix
    Processing helix  chain 'R' and resid 195 through 229
      removed outlier: 3.906A  pdb=" N   ARG R 199 " --> pdb=" O   ASP R 195 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 244 through 275
      Proline residue:  R 264  - end of helix
    Processing helix  chain 'R' and resid 282 through 305
      removed outlier: 4.429A  pdb=" N   MET R 292 " --> pdb=" O   PHE R 288 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   TRP R 295 " --> pdb=" O   ARG R 291 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ASN R 296 " --> pdb=" O   MET R 292 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 313
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.899A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.414A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.993A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.620A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.071A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.108A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.528A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.674A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.515A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.542A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 59 through 60
      removed outlier: 6.637A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 178 through 179

    397 hydrogen bonds defined for protein.
    1143 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.29

  Time building geometry restraints manager: 2.10 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1760
        1.33 -     1.45: 1435
        1.45 -     1.57: 3934
        1.57 -     1.69: 0
        1.69 -     1.81: 71
  Bond restraints: 7200
  Sorted by residual:
  bond pdb=" C02 7WT R 401 "
       pdb=" O01 7WT R 401 "
    ideal  model  delta    sigma   weight residual
    1.414  1.538 -0.124 2.00e-02 2.50e+03 3.85e+01
  bond pdb=" CA  ALA R 293 "
       pdb=" CB  ALA R 293 "
    ideal  model  delta    sigma   weight residual
    1.532  1.477  0.055 1.62e-02 3.81e+03 1.14e+01
  bond pdb=" C20 7WT R 401 "
       pdb=" C21 7WT R 401 "
    ideal  model  delta    sigma   weight residual
    1.497  1.556 -0.059 2.00e-02 2.50e+03 8.80e+00
  bond pdb=" CA  ALA R 289 "
       pdb=" CB  ALA R 289 "
    ideal  model  delta    sigma   weight residual
    1.530  1.482  0.049 1.69e-02 3.50e+03 8.30e+00
  bond pdb=" C22 7WT R 401 "
       pdb=" C23 7WT R 401 "
    ideal  model  delta    sigma   weight residual
    1.496  1.550 -0.054 2.00e-02 2.50e+03 7.20e+00
  ... (remaining 7195 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.74: 9729
        2.74 -     5.48: 61
        5.48 -     8.23: 4
        8.23 -    10.97: 3
       10.97 -    13.71: 1
  Bond angle restraints: 9798
  Sorted by residual:
  angle pdb=" N   LEU R 290 "
        pdb=" CA  LEU R 290 "
        pdb=" C   LEU R 290 "
      ideal   model   delta    sigma   weight residual
     111.36  102.64    8.72 1.09e+00 8.42e-01 6.40e+01
  angle pdb=" N   MET R 292 "
        pdb=" CA  MET R 292 "
        pdb=" C   MET R 292 "
      ideal   model   delta    sigma   weight residual
     113.38  107.19    6.19 1.23e+00 6.61e-01 2.53e+01
  angle pdb=" N   ALA R 293 "
        pdb=" CA  ALA R 293 "
        pdb=" C   ALA R 293 "
      ideal   model   delta    sigma   weight residual
     112.04  105.37    6.67 1.44e+00 4.82e-01 2.15e+01
  angle pdb=" C20 7WT R 401 "
        pdb=" C21 7WT R 401 "
        pdb=" C22 7WT R 401 "
      ideal   model   delta    sigma   weight residual
     128.03  114.32   13.71 3.00e+00 1.11e-01 2.09e+01
  angle pdb=" N   LEU R 287 "
        pdb=" CA  LEU R 287 "
        pdb=" C   LEU R 287 "
      ideal   model   delta    sigma   weight residual
     111.36  107.22    4.14 1.09e+00 8.42e-01 1.45e+01
  ... (remaining 9793 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.89: 3607
       15.89 -    31.77: 435
       31.77 -    47.66: 134
       47.66 -    63.55: 21
       63.55 -    79.44: 7
  Dihedral angle restraints: 4204
    sinusoidal: 1438
      harmonic: 2766
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -142.92   56.92     1      1.00e+01 1.00e-02 4.36e+01
  dihedral pdb=" CA  ARG R 100 "
           pdb=" C   ARG R 100 "
           pdb=" N   PHE R 101 "
           pdb=" CA  PHE R 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.29   24.71     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  CYS N  99 "
           pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   13.87   65.13     1      2.00e+01 2.50e-03 1.39e+01
  ... (remaining 4201 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1079
       0.078 -    0.156: 86
       0.156 -    0.234: 2
       0.234 -    0.312: 1
       0.312 -    0.391: 2
  Chirality restraints: 1170
  Sorted by residual:
  chirality pdb=" C03 7WT R 401 "
            pdb=" C02 7WT R 401 "
            pdb=" C04 7WT R 401 "
            pdb=" C20 7WT R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.92    0.39 2.00e-01 2.50e+01 3.81e+00
  chirality pdb=" C04 7WT R 401 "
            pdb=" C03 7WT R 401 "
            pdb=" C05 7WT R 401 "
            pdb=" C08 7WT R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.63    2.97   -0.34 2.00e-01 2.50e+01 2.97e+00
  chirality pdb=" CA  LEU R 290 "
            pdb=" N   LEU R 290 "
            pdb=" C   LEU R 290 "
            pdb=" CB  LEU R 290 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.73e+00
  ... (remaining 1167 not shown)

  Planarity restraints: 1222
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  87 "    0.010 2.00e-02 2.50e+03   1.91e-02 3.64e+00
        pdb=" C   THR B  87 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   THR B  87 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ASN B  88 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "   -0.028 5.00e-02 4.00e+02   4.20e-02 2.82e+00
        pdb=" N   PRO G  49 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO B 236 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1219 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1627
        2.78 -     3.31: 6367
        3.31 -     3.84: 11555
        3.84 -     4.37: 12921
        4.37 -     4.90: 23796
  Nonbonded interactions: 56266
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   SER N 112 "
            pdb=" NH2 ARG N 118 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   MET B 188 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OD2 ASP A  33 "
            pdb=" NZ  LYS B  78 "
     model   vdw
     2.271 3.120
  ... (remaining 56261 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.760
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
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      :  0.004   0.124   7200  Z= 0.253
  Angle     :  0.586  13.711   9798  Z= 0.324
  Chirality :  0.045   0.391   1170
  Planarity :  0.004   0.064   1222
  Dihedral  : 15.453  79.436   2401
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 18.83 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.28), residues: 930
  helix:  3.05 (0.27), residues: 354
  sheet:  0.50 (0.36), residues: 202
  loop : -1.01 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.015   0.001   PHE R 101 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.008   0.000   ARG R  57 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 118
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
REVERT: R  217 LEU cc_start: 0.8668 (tp) cc_final: 0.8225 (tp)
REVERT: R  291 ARG cc_start: 0.8164 (ptp-170) cc_final: 0.6998 (ptm160)
  outliers start: 2
  outliers final: 1
  residues processed: 119
  average time/residue: 0.2244
  time to fit residues: 34.5703
Evaluate side-chains
  115 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  287 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 28 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 392 ASN
R 189 ASN
R 243 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.133201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.113929 restraints weight = 9579.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.46
r_work: 0.3224 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.0661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7200  Z= 0.220
  Angle     :  0.480   6.140   9798  Z= 0.264
  Chirality :  0.041   0.132   1170
  Planarity :  0.003   0.043   1222
  Dihedral  :  5.157  55.267   1048
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 17.66 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.28), residues: 930
  helix:  2.90 (0.27), residues: 364
  sheet:  0.46 (0.36), residues: 203
  loop : -1.06 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.017   0.001   PHE B 199 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.005   0.000   ARG R 183 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
REVERT: A  378 ASP cc_start: 0.8097 (m-30) cc_final: 0.7692 (m-30)
REVERT: B  237 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8524 (p0)
REVERT: B  336 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8647 (tt)
REVERT: R  115 MET cc_start: 0.8697 (mmm) cc_final: 0.8270 (tpt)
REVERT: R  246 GLU cc_start: 0.7888 (mp0) cc_final: 0.7270 (tp30)
REVERT: R  291 ARG cc_start: 0.8121 (ptp-170) cc_final: 0.6776 (ptm160)
  outliers start: 19
  outliers final: 10
  residues processed: 134
  average time/residue: 0.2136
  time to fit residues: 37.8713
Evaluate side-chains
  127 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  287 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 7 optimal weight:    0.1980
   chunk 22 optimal weight:    5.9990
   chunk 39 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 90 optimal weight:    0.2980
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.135135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.115256 restraints weight = 9601.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 1.51
r_work: 0.3246 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.0847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7200  Z= 0.172
  Angle     :  0.448   5.650   9798  Z= 0.248
  Chirality :  0.040   0.134   1170
  Planarity :  0.003   0.042   1222
  Dihedral  :  4.854  52.307   1048
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.55 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.39 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.28), residues: 930
  helix:  3.10 (0.27), residues: 358
  sheet:  0.50 (0.36), residues: 202
  loop : -1.00 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.015   0.001   PHE R 101 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.004   0.000   ARG R  57 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
REVERT: B  237 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8420 (p0)
REVERT: B  336 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8569 (tt)
REVERT: R   56 GLN cc_start: 0.7723 (mm110) cc_final: 0.7317 (mm-40)
REVERT: R   59 ARG cc_start: 0.8027 (tmm-80) cc_final: 0.7531 (ttp-170)
REVERT: R  115 MET cc_start: 0.8707 (mmm) cc_final: 0.8264 (tpt)
REVERT: R  246 GLU cc_start: 0.7885 (mp0) cc_final: 0.7240 (tp30)
  outliers start: 17
  outliers final: 8
  residues processed: 129
  average time/residue: 0.2104
  time to fit residues: 35.9850
Evaluate side-chains
  124 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  208 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 16 optimal weight:    0.0000
   chunk 57 optimal weight:    1.9990
   chunk 13 optimal weight:    0.1980
   chunk 82 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   overall best weight:    0.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
R 180 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.135552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.115557 restraints weight = 9666.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 1.53
r_work: 0.3023 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.0994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7200  Z= 0.160
  Angle     :  0.435   5.436   9798  Z= 0.239
  Chirality :  0.040   0.133   1170
  Planarity :  0.003   0.040   1222
  Dihedral  :  4.360  29.047   1046
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.33 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 18.39 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.28), residues: 930
  helix:  3.20 (0.26), residues: 359
  sheet:  0.46 (0.36), residues: 210
  loop : -1.01 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.016   0.001   PHE R 101 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.006   0.000   ARG R  57 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.768 
Fit side-chains
REVERT: B  237 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8472 (p0)
REVERT: B  336 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8388 (tt)
REVERT: R   56 GLN cc_start: 0.7520 (mm110) cc_final: 0.7136 (mm-40)
REVERT: R   59 ARG cc_start: 0.7967 (tmm-80) cc_final: 0.7477 (ttp-170)
REVERT: R  115 MET cc_start: 0.8637 (mmm) cc_final: 0.8121 (tpt)
REVERT: R  246 GLU cc_start: 0.7855 (mp0) cc_final: 0.6989 (tp30)
  outliers start: 20
  outliers final: 13
  residues processed: 132
  average time/residue: 0.2067
  time to fit residues: 35.9106
Evaluate side-chains
  127 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue  133 ARG
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  208 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 84 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0470
   chunk 20 optimal weight:    0.9980
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
R 189 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.135231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.115303 restraints weight = 9541.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 1.51
r_work: 0.3022 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.1083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7200  Z= 0.173
  Angle     :  0.444   5.336   9798  Z= 0.244
  Chirality :  0.040   0.147   1170
  Planarity :  0.003   0.041   1222
  Dihedral  :  4.312  29.312   1046
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.55 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 18.25 %
    Favored  : 78.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.28), residues: 930
  helix:  3.20 (0.26), residues: 358
  sheet:  0.46 (0.36), residues: 203
  loop : -1.04 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.016   0.001   PHE R 101 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.006   0.000   ARG R 229 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
REVERT: B  237 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8481 (p0)
REVERT: B  336 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8394 (tt)
REVERT: R   56 GLN cc_start: 0.7539 (mm110) cc_final: 0.7153 (mm-40)
REVERT: R   59 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7428 (ttp-170)
REVERT: R  115 MET cc_start: 0.8669 (mmm) cc_final: 0.8141 (tpt)
REVERT: R  246 GLU cc_start: 0.7849 (mp0) cc_final: 0.6959 (tp30)
  outliers start: 21
  outliers final: 12
  residues processed: 128
  average time/residue: 0.2104
  time to fit residues: 35.8578
Evaluate side-chains
  125 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  208 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 91 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
R 189 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.134084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.114105 restraints weight = 9687.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 1.52
r_work: 0.3228 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.1169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7200  Z= 0.202
  Angle     :  0.460   5.320   9798  Z= 0.252
  Chirality :  0.041   0.147   1170
  Planarity :  0.003   0.043   1222
  Dihedral  :  4.275  28.679   1046
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.66 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 19.71 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.28), residues: 930
  helix:  3.21 (0.26), residues: 358
  sheet:  0.41 (0.35), residues: 210
  loop : -1.10 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP N  47 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.016   0.001   PHE R 101 
 TYR   0.011   0.001   TYR N  95 
 ARG   0.006   0.000   ARG R  57 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
REVERT: B  237 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8500 (p0)
REVERT: B  336 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8557 (tt)
REVERT: R   56 GLN cc_start: 0.7702 (mm110) cc_final: 0.7301 (mm-40)
REVERT: R   59 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7521 (ttp-170)
REVERT: R  200 PHE cc_start: 0.8421 (t80) cc_final: 0.7979 (t80)
REVERT: R  246 GLU cc_start: 0.7885 (mp0) cc_final: 0.7205 (tp30)
  outliers start: 17
  outliers final: 13
  residues processed: 126
  average time/residue: 0.2111
  time to fit residues: 35.2396
Evaluate side-chains
  127 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  208 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 72 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 271 ASN
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.132789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.112866 restraints weight = 9664.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 1.50
r_work: 0.2999 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7200  Z= 0.243
  Angle     :  0.482   5.316   9798  Z= 0.264
  Chirality :  0.042   0.147   1170
  Planarity :  0.003   0.049   1222
  Dihedral  :  4.328  27.869   1046
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.55 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 19.12 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.28), residues: 930
  helix:  3.07 (0.27), residues: 364
  sheet:  0.33 (0.36), residues: 206
  loop : -1.14 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.016   0.001   PHE R 101 
 TYR   0.012   0.001   TYR N  95 
 ARG   0.007   0.000   ARG R  57 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.855 
Fit side-chains
REVERT: B  237 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8689 (p0)
REVERT: B  336 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8470 (tt)
REVERT: R   56 GLN cc_start: 0.7632 (mm110) cc_final: 0.7317 (mm-40)
REVERT: R   59 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7319 (ttp-170)
REVERT: R  200 PHE cc_start: 0.8332 (t80) cc_final: 0.8027 (t80)
REVERT: R  246 GLU cc_start: 0.7848 (mp0) cc_final: 0.6979 (tp30)
  outliers start: 21
  outliers final: 14
  residues processed: 126
  average time/residue: 0.2089
  time to fit residues: 35.1892
Evaluate side-chains
  124 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue  133 ARG
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  287 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0010
   chunk 85 optimal weight:    4.9990
   chunk 47 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.6786

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

Flipped N/Q/H residues before XYZ refinement:
G  44 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.134157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.114269 restraints weight = 9622.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 1.51
r_work: 0.3232 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7200  Z= 0.183
  Angle     :  0.454   5.216   9798  Z= 0.249
  Chirality :  0.041   0.144   1170
  Planarity :  0.003   0.047   1222
  Dihedral  :  4.191  24.695   1046
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.66 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 18.98 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.28), residues: 930
  helix:  3.26 (0.26), residues: 358
  sheet:  0.39 (0.36), residues: 210
  loop : -1.13 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.017   0.001   PHE R 101 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.007   0.000   ARG R  57 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ARG cc_start: 0.7310 (mmm-85) cc_final: 0.6914 (tpp80)
REVERT: B  237 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8461 (p0)
REVERT: B  336 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8527 (tt)
REVERT: R   56 GLN cc_start: 0.7662 (mm110) cc_final: 0.7254 (mm-40)
REVERT: R   59 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7518 (ttp-170)
REVERT: R  200 PHE cc_start: 0.8425 (t80) cc_final: 0.8009 (t80)
REVERT: R  217 LEU cc_start: 0.8584 (tp) cc_final: 0.8150 (tp)
REVERT: R  246 GLU cc_start: 0.7789 (mp0) cc_final: 0.7143 (tp30)
  outliers start: 20
  outliers final: 14
  residues processed: 129
  average time/residue: 0.2025
  time to fit residues: 34.5755
Evaluate side-chains
  128 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue  133 ARG
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  287 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.1384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.131571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.112318 restraints weight = 9835.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 1.45
r_work: 0.3180 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7200  Z= 0.270
  Angle     :  0.512   6.385   9798  Z= 0.276
  Chirality :  0.042   0.149   1170
  Planarity :  0.004   0.051   1222
  Dihedral  :  4.323  25.431   1046
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.98 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 19.42 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.28), residues: 930
  helix:  3.08 (0.27), residues: 364
  sheet:  0.31 (0.36), residues: 206
  loop : -1.12 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.017   0.001   PHE B 199 
 TYR   0.012   0.001   TYR N  95 
 ARG   0.008   0.000   ARG R  57 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.741 
Fit side-chains
REVERT: A   22 ARG cc_start: 0.7452 (mmm-85) cc_final: 0.7041 (tpp80)
REVERT: A  293 LYS cc_start: 0.9116 (mttp) cc_final: 0.8902 (mttp)
REVERT: B  237 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8591 (p0)
REVERT: B  336 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8562 (tt)
REVERT: R   56 GLN cc_start: 0.7719 (mm110) cc_final: 0.7356 (mm-40)
REVERT: R   59 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7448 (ttp-170)
REVERT: R  200 PHE cc_start: 0.8475 (t80) cc_final: 0.8187 (t80)
REVERT: R  217 LEU cc_start: 0.8628 (tp) cc_final: 0.8204 (tp)
REVERT: R  246 GLU cc_start: 0.7724 (mp0) cc_final: 0.7122 (tp30)
  outliers start: 17
  outliers final: 14
  residues processed: 121
  average time/residue: 0.2078
  time to fit residues: 33.1088
Evaluate side-chains
  123 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue  133 ARG
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  287 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 7 optimal weight:    0.4980
   chunk 83 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0040
   chunk 56 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.135004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.115003 restraints weight = 9828.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 1.53
r_work: 0.3237 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.1358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7200  Z= 0.169
  Angle     :  0.467   6.544   9798  Z= 0.252
  Chirality :  0.041   0.144   1170
  Planarity :  0.003   0.046   1222
  Dihedral  :  4.112  24.979   1046
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.76 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 19.12 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.28), residues: 930
  helix:  3.28 (0.26), residues: 359
  sheet:  0.46 (0.36), residues: 209
  loop : -1.14 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.017   0.001   PHE R 101 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.008   0.000   ARG R  57 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.818 
Fit side-chains
REVERT: A   22 ARG cc_start: 0.7292 (mmm-85) cc_final: 0.6915 (tpp80)
REVERT: A  378 ASP cc_start: 0.8124 (m-30) cc_final: 0.7696 (m-30)
REVERT: B  237 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8444 (p0)
REVERT: B  336 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8623 (tt)
REVERT: R   56 GLN cc_start: 0.7656 (mm110) cc_final: 0.7241 (mm-40)
REVERT: R   59 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7518 (ttp-170)
REVERT: R  200 PHE cc_start: 0.8425 (t80) cc_final: 0.8036 (t80)
REVERT: R  217 LEU cc_start: 0.8571 (tp) cc_final: 0.8149 (tp)
REVERT: R  246 GLU cc_start: 0.7716 (mp0) cc_final: 0.7080 (tp30)
  outliers start: 18
  outliers final: 15
  residues processed: 124
  average time/residue: 0.2068
  time to fit residues: 34.0937
Evaluate side-chains
  128 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  240 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  237 ASN
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain R residue  133 ARG
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  179 ILE
Chi-restraints excluded: chain R residue  208 LEU
Chi-restraints excluded: chain R residue  287 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0470
   chunk 36 optimal weight:    3.9990
   chunk 66 optimal weight:    0.5980
   chunk 62 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 77 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0370
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.3956

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.136850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.117126 restraints weight = 9615.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.50
r_work: 0.3266 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7200  Z= 0.145
  Angle     :  0.457   6.451   9798  Z= 0.245
  Chirality :  0.040   0.151   1170
  Planarity :  0.003   0.040   1222
  Dihedral  :  3.937  22.421   1046
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.12 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 19.56 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.28), residues: 930
  helix:  3.34 (0.26), residues: 359
  sheet:  0.53 (0.35), residues: 210
  loop : -1.16 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.000   HIS A 357 
 PHE   0.017   0.001   PHE R  78 
 TYR   0.009   0.001   TYR N  95 
 ARG   0.008   0.000   ARG R  57 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3580.82 seconds
wall clock time: 64 minutes 28.36 seconds (3868.36 seconds total)