Starting phenix.real_space_refine
on Wed Mar  4 13:36:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ckz_30395/03_2026/7ckz_30395.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ckz_30395/03_2026/7ckz_30395.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ckz_30395/03_2026/7ckz_30395.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ckz_30395/03_2026/7ckz_30395.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ckz_30395/03_2026/7ckz_30395.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ckz_30395/03_2026/7ckz_30395.cif"
  }
  resolution = 3.1
  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
-------------------------------------------------------------------------------
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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 7222 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     Cl      2      4.86       5
     C    5180      2.51       5
     N    1406      2.21       5
     O    1492      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8133
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1906
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 30
    Chain: "B"
      Number of atoms: 2587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2587
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "G"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 438
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "N"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 970
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 2163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2163
          Classifications: {'peptide': 275}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 9, 'TRANS': 265}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "R"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 69
          Unusual residues: {'CLR': 1, 'G4C': 1, 'LDP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.09, per 1000 atoms: 0.26
  Number of scatterers: 8133
  At special positions: 0
  Unit cell: (96, 80, 125, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      53     16.00
     O    1492      8.00
     N    1406      7.00
     C    5180      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, 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  96 " - pdb=" SG  CYS R 186 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R 298 " - pdb=" SG  CYS R 307 " 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: 0.72
  Conformation dependent library (CDL) restraints added in 305.6 milliseconds
  

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      43.1% alpha, 18.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 40
      removed outlier: 3.864A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 59
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 281 through 285
      removed outlier: 4.155A  pdb=" N   THR A 284 " --> pdb=" O   TRP A 281 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ILE A 285 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 281 through 285'
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 4.357A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   VAL A 301 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 5.819A  pdb=" N   LEU A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 316
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.756A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.521A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 25
    Processing helix  chain 'B' and resid 29 through 33
      removed outlier: 3.828A  pdb=" N   ILE B  33 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 24
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.705A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.992A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 23 through 51
      removed outlier: 3.572A  pdb=" N   PHE R  51 " --> pdb=" O   ALA R  47 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 57 through 76
      removed outlier: 3.624A  pdb=" N   PHE R  61 " --> pdb=" O   LYS R  57 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   PHE R  62 " --> pdb=" O   VAL R  58 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   VAL R  63 " --> pdb=" O   THR R  59 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 77 through 88
    Processing helix  chain 'R' and resid 92 through 94
      No H-bonds generated for 'chain 'R' and resid 92 through 94'
    Processing helix  chain 'R' and resid 95 through 127
    Processing helix  chain 'R' and resid 127 through 135
    Processing helix  chain 'R' and resid 136 through 161
      removed outlier: 4.621A  pdb=" N   ILE R 157 " --> pdb=" O   LEU R 153 " (cutoff:3.500A)
      Proline residue:  R 158  - end of helix
    Processing helix  chain 'R' and resid 191 through 203
      removed outlier: 3.849A  pdb=" N   SER R 197 " --> pdb=" O   THR R 193 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   VAL R 200 " --> pdb=" O   ILE R 196 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ILE R 201 " --> pdb=" O   SER R 197 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 203 through 237
      removed outlier: 4.324A  pdb=" N   ALA R 234 " --> pdb=" O   ALA R 230 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 264 through 278
      removed outlier: 4.016A  pdb=" N   LYS R 269 " --> pdb=" O   LYS R 265 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU R 271 " --> pdb=" O   GLU R 267 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 278 through 293
      Proline residue:  R 287  - end of helix
      removed outlier: 3.882A  pdb=" N   LEU R 291 " --> pdb=" O   PRO R 287 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 294 through 298
    Processing helix  chain 'R' and resid 309 through 331
      removed outlier: 4.129A  pdb=" N   VAL R 315 " --> pdb=" O   ASN R 311 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   PHE R 316 " --> pdb=" O   THR R 312 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ASN R 323 " --> pdb=" O   PHE R 319 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   SER R 324 " --> pdb=" O   GLY R 320 " (cutoff:3.500A)
      Proline residue:  R 328  - end of helix
    Processing helix  chain 'R' and resid 334 through 344
      removed outlier: 3.932A  pdb=" N   ALA R 340 " --> pdb=" O   ASP R 336 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   THR R 343 " --> pdb=" O   LYS R 339 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214
      removed outlier: 3.505A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.899A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.714A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.901A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 4.039A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.644A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.584A  pdb=" N   PHE B 222 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.890A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.188A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 5.891A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8
      removed outlier: 3.701A  pdb=" N   LEU N  20 " --> pdb=" O   LEU N  81 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU N  81 " --> pdb=" O   LEU N  20 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 5.498A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    412 hydrogen bonds defined for protein.
    1167 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: 1.25

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1304
        1.31 -     1.44: 2324
        1.44 -     1.57: 4601
        1.57 -     1.70: 1
        1.70 -     1.82: 74
  Bond restraints: 8304
  Sorted by residual:
  bond pdb=" C05 G4C R 503 "
       pdb=" N04 G4C R 503 "
    ideal  model  delta    sigma   weight residual
    1.355  1.481 -0.126 2.00e-02 2.50e+03 3.96e+01
  bond pdb=" C16 G4C R 503 "
       pdb=" C18 G4C R 503 "
    ideal  model  delta    sigma   weight residual
    1.508  1.594 -0.086 2.00e-02 2.50e+03 1.83e+01
  bond pdb=" N   ARG N 105 "
       pdb=" CA  ARG N 105 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.18e-02 7.18e+03 7.80e+00
  bond pdb=" N   PHE B 234 "
       pdb=" CA  PHE B 234 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.031 1.25e-02 6.40e+03 6.34e+00
  bond pdb=" C08 G4C R 503 "
       pdb="CL9  G4C R 503 "
    ideal  model  delta    sigma   weight residual
    1.735  1.785 -0.050 2.00e-02 2.50e+03 6.18e+00
  ... (remaining 8299 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 11131
        1.88 -     3.75: 118
        3.75 -     5.63: 16
        5.63 -     7.50: 4
        7.50 -     9.38: 1
  Bond angle restraints: 11270
  Sorted by residual:
  angle pdb=" C03 G4C R 503 "
        pdb=" N04 G4C R 503 "
        pdb=" C05 G4C R 503 "
      ideal   model   delta    sigma   weight residual
     118.75  128.13   -9.38 3.00e+00 1.11e-01 9.77e+00
  angle pdb=" N   ARG N 105 "
        pdb=" CA  ARG N 105 "
        pdb=" C   ARG N 105 "
      ideal   model   delta    sigma   weight residual
     112.72  109.57    3.15 1.14e+00 7.69e-01 7.61e+00
  angle pdb=" N   VAL R 276 "
        pdb=" CA  VAL R 276 "
        pdb=" C   VAL R 276 "
      ideal   model   delta    sigma   weight residual
     111.81  109.50    2.31 8.60e-01 1.35e+00 7.24e+00
  angle pdb=" C06 G4C R 503 "
        pdb=" C05 G4C R 503 "
        pdb=" N04 G4C R 503 "
      ideal   model   delta    sigma   weight residual
     116.82  124.06   -7.24 3.00e+00 1.11e-01 5.82e+00
  angle pdb=" C03 G4C R 503 "
        pdb=" N04 G4C R 503 "
        pdb=" C16 G4C R 503 "
      ideal   model   delta    sigma   weight residual
     119.52  112.47    7.05 3.00e+00 1.11e-01 5.53e+00
  ... (remaining 11265 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.78: 4656
       21.78 -    43.56: 271
       43.56 -    65.34: 38
       65.34 -    87.12: 10
       87.12 -   108.90: 6
  Dihedral angle restraints: 4981
    sinusoidal: 1959
      harmonic: 3022
  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  -35.36  -50.64     1      1.00e+01 1.00e-02 3.51e+01
  dihedral pdb=" CB  CYS R  96 "
           pdb=" SG  CYS R  96 "
           pdb=" SG  CYS R 186 "
           pdb=" CB  CYS R 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   58.75   34.25     1      1.00e+01 1.00e-02 1.66e+01
  dihedral pdb=" C02 G4C R 503 "
           pdb=" C03 G4C R 503 "
           pdb=" C30 G4C R 503 "
           pdb=" C19 G4C R 503 "
      ideal   model   delta sinusoidal    sigma   weight residual
      66.31  175.21 -108.90     1      3.00e+01 1.11e-03 1.41e+01
  ... (remaining 4978 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 796
       0.031 -    0.062: 351
       0.062 -    0.093: 94
       0.093 -    0.124: 37
       0.124 -    0.155: 4
  Chirality restraints: 1282
  Sorted by residual:
  chirality pdb=" C16 G4C R 503 "
            pdb=" C17 G4C R 503 "
            pdb=" C18 G4C R 503 "
            pdb=" N04 G4C R 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.62    0.15 2.00e-01 2.50e+01 5.98e-01
  chirality pdb=" CB  VAL N 110 "
            pdb=" CA  VAL N 110 "
            pdb=" CG1 VAL N 110 "
            pdb=" CG2 VAL N 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.44e-01
  chirality pdb=" CA  ILE B 232 "
            pdb=" N   ILE B 232 "
            pdb=" C   ILE B 232 "
            pdb=" CB  ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.43e-01
  ... (remaining 1279 not shown)

  Planarity restraints: 1422
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 205 "    0.025 5.00e-02 4.00e+02   3.82e-02 2.33e+00
        pdb=" N   PRO R 206 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO R 206 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO R 206 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 331 "   -0.021 5.00e-02 4.00e+02   3.25e-02 1.69e+00
        pdb=" N   PRO A 332 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 332 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 332 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "   -0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO G  49 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1419 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.24: 10
        2.24 -     2.90: 3347
        2.90 -     3.57: 12622
        3.57 -     4.23: 21827
        4.23 -     4.90: 35825
  Nonbonded interactions: 73631
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 119 "
            pdb=" O   GLY B 144 "
     model   vdw
     1.570 3.040
  nonbonded pdb=" OD1 ASN B 119 "
            pdb=" C   GLY B 144 "
     model   vdw
     1.910 3.270
  nonbonded pdb=" OG  SER R 202 "
            pdb=" O2  LDP R 502 "
     model   vdw
     2.070 3.040
  nonbonded pdb=" O   ILE R 154 "
            pdb=" OH  TYR R 194 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" O   ALA R 101 "
            pdb=" OG  SER R 155 "
     model   vdw
     2.179 3.040
  ... (remaining 73626 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:             0.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.320
  Find NCS groups from input model:        0.030
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6892
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      :  0.003   0.126   8308  Z= 0.178
  Angle     :  0.519   9.377  11278  Z= 0.296
  Chirality :  0.039   0.155   1282
  Planarity :  0.003   0.038   1422
  Dihedral  : 14.328 108.900   3005
  Min Nonbonded Distance : 1.570

Molprobity Statistics.
  All-atom Clashscore : 23.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  8.14 %
    Favored  : 90.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.38 (0.23), residues: 1017
  helix: -1.83 (0.21), residues: 396
  sheet: -2.71 (0.31), residues: 200
  loop : -2.20 (0.28), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  52 
 TYR   0.009   0.001   TYR N 117 
 PHE   0.009   0.001   PHE R  20 
 TRP   0.011   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8304)
  covalent geometry    : angle       0.51878 (11270)
  SS BOND              : bond        0.00779 (    4)
  SS BOND              : angle       1.07279 (    8)
  hydrogen bonds       : bond        0.22163 (  412)
  hydrogen bonds       : angle       8.40715 ( 1167)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 270
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 PHE cc_start: 0.5446 (t80) cc_final: 0.4476 (t80)
REVERT: A  339 TYR cc_start: 0.8230 (m-80) cc_final: 0.7802 (m-80)
REVERT: A  343 ASP cc_start: 0.7415 (m-30) cc_final: 0.7082 (m-30)
REVERT: A  386 MET cc_start: 0.7538 (ttp) cc_final: 0.7273 (ttm)
REVERT: B  247 ASP cc_start: 0.8084 (p0) cc_final: 0.7806 (p0)
REVERT: N   94 TYR cc_start: 0.8186 (m-80) cc_final: 0.7947 (m-80)
REVERT: N   95 TYR cc_start: 0.8270 (m-80) cc_final: 0.7960 (m-80)
REVERT: R  156 PHE cc_start: 0.6519 (m-10) cc_final: 0.5908 (m-80)
REVERT: R  292 ASN cc_start: 0.8348 (t0) cc_final: 0.8067 (t0)
  outliers start: 8
  outliers final: 3
  residues processed: 274
  average time/residue: 0.1171
  time to fit residues: 41.0803
Evaluate side-chains
  211 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 208
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.0970
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0050
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.3980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.4592

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A  41 HIS
A 267 GLN
A 271 ASN
A 278 ASN
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 259 GLN
B 266 HIS
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  44 HIS
N  13 GLN
N  31 ASN
N  39 GLN
** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.189878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.157613 restraints weight = 9321.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3810 rms_B_bonded: 2.05
r_work: 0.3667 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8308  Z= 0.153
  Angle     :  0.592  13.506  11278  Z= 0.304
  Chirality :  0.043   0.313   1282
  Planarity :  0.004   0.043   1422
  Dihedral  :  7.257  78.358   1215
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.16 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.21 (0.25), residues: 1017
  helix: -0.49 (0.25), residues: 397
  sheet: -2.71 (0.32), residues: 198
  loop : -1.62 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 227 
 TYR   0.010   0.002   TYR B 264 
 PHE   0.014   0.001   PHE B 151 
 TRP   0.014   0.001   TRP B 211 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8304)
  covalent geometry    : angle       0.59162 (11270)
  SS BOND              : bond        0.00181 (    4)
  SS BOND              : angle       0.86537 (    8)
  hydrogen bonds       : bond        0.04960 (  412)
  hydrogen bonds       : angle       5.93555 ( 1167)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 223
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8251 (tppt) cc_final: 0.7684 (mmtm)
REVERT: A  222 PHE cc_start: 0.5887 (t80) cc_final: 0.4992 (t80)
REVERT: A  255 MET cc_start: 0.0640 (mmm) cc_final: -0.1735 (mtp)
REVERT: A  318 TYR cc_start: 0.7407 (t80) cc_final: 0.7075 (t80)
REVERT: A  339 TYR cc_start: 0.8560 (m-80) cc_final: 0.7853 (m-80)
REVERT: A  343 ASP cc_start: 0.7924 (m-30) cc_final: 0.7597 (m-30)
REVERT: B  124 TYR cc_start: 0.8759 (m-80) cc_final: 0.8449 (m-80)
REVERT: B  209 LYS cc_start: 0.8801 (mttp) cc_final: 0.8584 (mmtm)
REVERT: B  228 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6831 (m-30)
REVERT: B  323 ASP cc_start: 0.7560 (p0) cc_final: 0.7050 (p0)
REVERT: B  337 LYS cc_start: 0.8305 (mmtp) cc_final: 0.8045 (mptt)
REVERT: R  142 ILE cc_start: 0.7429 (mt) cc_final: 0.7208 (mt)
REVERT: R  156 PHE cc_start: 0.6750 (m-10) cc_final: 0.6054 (m-80)
REVERT: R  319 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7502 (t80)
  outliers start: 19
  outliers final: 13
  residues processed: 233
  average time/residue: 0.1075
  time to fit residues: 32.8381
Evaluate side-chains
  209 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 194
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  319 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 58 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0980
   chunk 33 optimal weight:    0.0670
   chunk 76 optimal weight:    0.7980
   chunk 16 optimal weight:    0.2980
   chunk 93 optimal weight:    0.9980
   overall best weight:    0.3718

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  29 GLN
A 236 GLN
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  44 HIS
N  31 ASN
R  60 ASN
** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.190416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.157053 restraints weight = 9246.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3803 rms_B_bonded: 2.11
r_work: 0.3682 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3532 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.2820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8308  Z= 0.139
  Angle     :  0.552   9.544  11278  Z= 0.284
  Chirality :  0.042   0.210   1282
  Planarity :  0.004   0.054   1422
  Dihedral  :  5.499  52.100   1215
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 18.95 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.69 (0.26), residues: 1017
  helix:  0.01 (0.26), residues: 404
  sheet: -2.32 (0.36), residues: 190
  loop : -1.53 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 265 
 TYR   0.014   0.002   TYR B 264 
 PHE   0.019   0.001   PHE B 151 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8304)
  covalent geometry    : angle       0.55179 (11270)
  SS BOND              : bond        0.00093 (    4)
  SS BOND              : angle       0.84074 (    8)
  hydrogen bonds       : bond        0.04137 (  412)
  hydrogen bonds       : angle       5.52130 ( 1167)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 210
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8278 (tppt) cc_final: 0.7768 (mmtm)
REVERT: A  208 PHE cc_start: 0.3354 (m-80) cc_final: 0.2702 (t80)
REVERT: A  222 PHE cc_start: 0.5638 (t80) cc_final: 0.5179 (t80)
REVERT: A  255 MET cc_start: 0.0771 (mmm) cc_final: -0.1370 (mtp)
REVERT: A  294 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7490 (mm-40)
REVERT: A  318 TYR cc_start: 0.7465 (t80) cc_final: 0.7169 (t80)
REVERT: A  332 PRO cc_start: 0.7875 (Cg_exo) cc_final: 0.7611 (Cg_endo)
REVERT: A  333 ARG cc_start: 0.8879 (mtp-110) cc_final: 0.8670 (mtp-110)
REVERT: A  339 TYR cc_start: 0.8608 (m-80) cc_final: 0.7940 (m-80)
REVERT: A  343 ASP cc_start: 0.8065 (m-30) cc_final: 0.7757 (m-30)
REVERT: A  363 PHE cc_start: 0.8963 (m-80) cc_final: 0.8618 (m-80)
REVERT: B  124 TYR cc_start: 0.8834 (m-80) cc_final: 0.8434 (m-80)
REVERT: B  228 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7116 (m-30)
REVERT: B  262 MET cc_start: 0.8545 (tpp) cc_final: 0.8253 (tpp)
REVERT: B  323 ASP cc_start: 0.7886 (p0) cc_final: 0.7416 (p0)
REVERT: G   21 MET cc_start: 0.7756 (mtp) cc_final: 0.7506 (ttt)
REVERT: G   29 LYS cc_start: 0.8329 (mmtm) cc_final: 0.7961 (mmtm)
REVERT: N   95 TYR cc_start: 0.8879 (m-80) cc_final: 0.8346 (m-80)
REVERT: R   81 LYS cc_start: 0.8375 (tptt) cc_final: 0.8001 (tptt)
REVERT: R  142 ILE cc_start: 0.7519 (mt) cc_final: 0.7216 (mt)
REVERT: R  154 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8248 (mt)
REVERT: R  319 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7477 (t80)
  outliers start: 32
  outliers final: 19
  residues processed: 222
  average time/residue: 0.1018
  time to fit residues: 29.8703
Evaluate side-chains
  213 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 191
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue   31 ASN
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain R residue   59 THR
Chi-restraints excluded: chain R residue   60 ASN
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  207 VAL
Chi-restraints excluded: chain R residue  211 ILE
Chi-restraints excluded: chain R residue  319 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 21 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9990
   chunk 24 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9990
   chunk 77 optimal weight:    6.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  29 GLN
A 371 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 323 ASN ** 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 = 0.4053 r_free = 0.4053 target = 0.181048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.146205 restraints weight = 9438.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 2.15
r_work: 0.3528 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3371 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   8308  Z= 0.200
  Angle     :  0.569   6.352  11278  Z= 0.298
  Chirality :  0.042   0.148   1282
  Planarity :  0.004   0.050   1422
  Dihedral  :  4.555  53.573   1213
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 17.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 19.30 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.26), residues: 1017
  helix:  0.23 (0.26), residues: 404
  sheet: -2.25 (0.36), residues: 185
  loop : -1.40 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 347 
 TYR   0.023   0.002   TYR B 264 
 PHE   0.015   0.002   PHE B 151 
 TRP   0.013   0.002   TRP B  63 
 HIS   0.006   0.002   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 8304)
  covalent geometry    : angle       0.56859 (11270)
  SS BOND              : bond        0.00277 (    4)
  SS BOND              : angle       1.18543 (    8)
  hydrogen bonds       : bond        0.04255 (  412)
  hydrogen bonds       : angle       5.43676 ( 1167)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 208
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8207 (tppt) cc_final: 0.7747 (mmtm)
REVERT: A  208 PHE cc_start: 0.3849 (m-80) cc_final: 0.3258 (t80)
REVERT: A  222 PHE cc_start: 0.6079 (t80) cc_final: 0.5398 (t80)
REVERT: A  318 TYR cc_start: 0.7686 (t80) cc_final: 0.7396 (t80)
REVERT: A  332 PRO cc_start: 0.7785 (Cg_exo) cc_final: 0.7435 (Cg_endo)
REVERT: A  333 ARG cc_start: 0.8905 (mtp-110) cc_final: 0.8577 (mtp-110)
REVERT: A  339 TYR cc_start: 0.8666 (m-80) cc_final: 0.8049 (m-80)
REVERT: A  343 ASP cc_start: 0.8188 (m-30) cc_final: 0.7960 (m-30)
REVERT: B  124 TYR cc_start: 0.9015 (m-80) cc_final: 0.8643 (m-80)
REVERT: B  176 GLN cc_start: 0.8330 (mt0) cc_final: 0.8107 (mt0)
REVERT: B  209 LYS cc_start: 0.9028 (mttp) cc_final: 0.8697 (mmtm)
REVERT: B  228 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7382 (m-30)
REVERT: B  262 MET cc_start: 0.8611 (tpp) cc_final: 0.8318 (tpp)
REVERT: B  323 ASP cc_start: 0.8134 (p0) cc_final: 0.7860 (p0)
REVERT: R  142 ILE cc_start: 0.7636 (mt) cc_final: 0.7337 (mt)
REVERT: R  154 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8265 (mt)
  outliers start: 34
  outliers final: 23
  residues processed: 228
  average time/residue: 0.1013
  time to fit residues: 30.8872
Evaluate side-chains
  208 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 183
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  202 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 89 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 25 optimal weight:    8.9990
   chunk 96 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  29 GLN
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 ASN
A 371 ASN
A 377 ASN
B  32 GLN
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.181531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.146681 restraints weight = 9380.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 2.14
r_work: 0.3542 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8308  Z= 0.172
  Angle     :  0.555   8.391  11278  Z= 0.291
  Chirality :  0.042   0.141   1282
  Planarity :  0.004   0.051   1422
  Dihedral  :  4.627  54.840   1213
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 17.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 21.05 %
    Favored  : 74.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.26), residues: 1017
  helix:  0.35 (0.26), residues: 398
  sheet: -2.20 (0.36), residues: 195
  loop : -1.18 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 347 
 TYR   0.017   0.002   TYR B 289 
 PHE   0.015   0.001   PHE B 151 
 TRP   0.013   0.002   TRP A 234 
 HIS   0.006   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 8304)
  covalent geometry    : angle       0.55433 (11270)
  SS BOND              : bond        0.00219 (    4)
  SS BOND              : angle       1.05783 (    8)
  hydrogen bonds       : bond        0.04124 (  412)
  hydrogen bonds       : angle       5.39862 ( 1167)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 193
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8321 (tppt) cc_final: 0.7835 (mmtm)
REVERT: A  208 PHE cc_start: 0.3933 (OUTLIER) cc_final: 0.3558 (t80)
REVERT: A  222 PHE cc_start: 0.5995 (t80) cc_final: 0.5428 (t80)
REVERT: A  318 TYR cc_start: 0.7666 (t80) cc_final: 0.7424 (t80)
REVERT: A  333 ARG cc_start: 0.8883 (mtp-110) cc_final: 0.8668 (mtp-110)
REVERT: A  338 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8281 (ttmt)
REVERT: A  339 TYR cc_start: 0.8709 (m-80) cc_final: 0.8052 (m-80)
REVERT: A  343 ASP cc_start: 0.8195 (m-30) cc_final: 0.7954 (m-30)
REVERT: A  378 ASP cc_start: 0.8174 (m-30) cc_final: 0.7963 (m-30)
REVERT: B  124 TYR cc_start: 0.9010 (m-80) cc_final: 0.8701 (m-80)
REVERT: B  243 THR cc_start: 0.8737 (p) cc_final: 0.8442 (p)
REVERT: B  262 MET cc_start: 0.8545 (tpp) cc_final: 0.8290 (tpp)
REVERT: B  323 ASP cc_start: 0.8073 (p0) cc_final: 0.7707 (p0)
REVERT: G   29 LYS cc_start: 0.8463 (tppt) cc_final: 0.7816 (mmtm)
REVERT: N   87 LYS cc_start: 0.7623 (mttt) cc_final: 0.7328 (mmtm)
REVERT: N   95 TYR cc_start: 0.8999 (m-80) cc_final: 0.8464 (m-80)
REVERT: R   81 LYS cc_start: 0.8537 (tptt) cc_final: 0.8096 (tptt)
REVERT: R  142 ILE cc_start: 0.7640 (mt) cc_final: 0.7321 (mt)
REVERT: R  154 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8277 (mt)
  outliers start: 40
  outliers final: 25
  residues processed: 217
  average time/residue: 0.0912
  time to fit residues: 26.8936
Evaluate side-chains
  210 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 182
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  202 SER
Chi-restraints excluded: chain R residue  207 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 97 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 77 optimal weight:    7.9990
   chunk 20 optimal weight:    0.0570
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
A 377 ASN
B  32 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  60 ASN
** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.181426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.147093 restraints weight = 9311.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 2.12
r_work: 0.3562 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3410 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.3615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8308  Z= 0.153
  Angle     :  0.547   7.825  11278  Z= 0.288
  Chirality :  0.042   0.165   1282
  Planarity :  0.004   0.051   1422
  Dihedral  :  4.668  54.456   1213
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 21.16 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.27), residues: 1017
  helix:  0.48 (0.26), residues: 402
  sheet: -1.99 (0.38), residues: 174
  loop : -1.12 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 347 
 TYR   0.016   0.002   TYR B 289 
 PHE   0.022   0.001   PHE A 363 
 TRP   0.013   0.002   TRP A 234 
 HIS   0.009   0.002   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8304)
  covalent geometry    : angle       0.54665 (11270)
  SS BOND              : bond        0.00200 (    4)
  SS BOND              : angle       0.96759 (    8)
  hydrogen bonds       : bond        0.04012 (  412)
  hydrogen bonds       : angle       5.29709 ( 1167)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 194
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8337 (tppt) cc_final: 0.7900 (mmtm)
REVERT: A   20 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7344 (ttm-80)
REVERT: A  208 PHE cc_start: 0.3906 (OUTLIER) cc_final: 0.3579 (t80)
REVERT: A  222 PHE cc_start: 0.5966 (t80) cc_final: 0.5452 (t80)
REVERT: A  255 MET cc_start: 0.1062 (mmm) cc_final: -0.1136 (mtp)
REVERT: A  292 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8142 (m-40)
REVERT: A  318 TYR cc_start: 0.7691 (t80) cc_final: 0.7457 (t80)
REVERT: A  333 ARG cc_start: 0.8888 (mtp-110) cc_final: 0.8687 (mtp-110)
REVERT: A  338 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8247 (ttmt)
REVERT: A  339 TYR cc_start: 0.8716 (m-80) cc_final: 0.8046 (m-80)
REVERT: A  343 ASP cc_start: 0.8153 (m-30) cc_final: 0.7931 (m-30)
REVERT: B  124 TYR cc_start: 0.8959 (m-80) cc_final: 0.8710 (m-80)
REVERT: B  197 ARG cc_start: 0.7969 (tpp80) cc_final: 0.7286 (tpp80)
REVERT: B  228 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7370 (m-30)
REVERT: B  243 THR cc_start: 0.8620 (p) cc_final: 0.8302 (p)
REVERT: B  323 ASP cc_start: 0.8016 (p0) cc_final: 0.7601 (p0)
REVERT: G   29 LYS cc_start: 0.8482 (tppt) cc_final: 0.7958 (tptt)
REVERT: N   80 TYR cc_start: 0.8525 (m-80) cc_final: 0.8171 (m-80)
REVERT: N   87 LYS cc_start: 0.7566 (mttt) cc_final: 0.7300 (mmtm)
REVERT: N   95 TYR cc_start: 0.8991 (m-80) cc_final: 0.8475 (m-80)
REVERT: R  125 ILE cc_start: 0.8428 (mm) cc_final: 0.7675 (mt)
REVERT: R  142 ILE cc_start: 0.7673 (mt) cc_final: 0.7333 (mt)
REVERT: R  154 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8255 (mt)
REVERT: R  163 TRP cc_start: 0.6040 (m100) cc_final: 0.5755 (m100)
  outliers start: 37
  outliers final: 20
  residues processed: 214
  average time/residue: 0.0973
  time to fit residues: 28.1431
Evaluate side-chains
  206 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 181
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   60 ASN
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  202 SER
Chi-restraints excluded: chain R residue  207 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 82 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 55 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
B  32 GLN
B 239 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  60 ASN
** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.178646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.143825 restraints weight = 9371.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.11
r_work: 0.3520 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3362 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.3791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8308  Z= 0.198
  Angle     :  0.581   7.957  11278  Z= 0.305
  Chirality :  0.043   0.154   1282
  Planarity :  0.004   0.051   1422
  Dihedral  :  4.800  53.881   1213
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 18.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 21.51 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.27), residues: 1017
  helix:  0.45 (0.26), residues: 401
  sheet: -1.96 (0.37), residues: 181
  loop : -1.06 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  38 
 TYR   0.015   0.002   TYR B 289 
 PHE   0.035   0.002   PHE A 363 
 TRP   0.014   0.002   TRP B  63 
 HIS   0.007   0.002   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 8304)
  covalent geometry    : angle       0.58070 (11270)
  SS BOND              : bond        0.00251 (    4)
  SS BOND              : angle       1.09400 (    8)
  hydrogen bonds       : bond        0.04155 (  412)
  hydrogen bonds       : angle       5.35193 ( 1167)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 199
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8303 (tppt) cc_final: 0.7901 (mmtm)
REVERT: A   20 ARG cc_start: 0.7623 (ttp80) cc_final: 0.7337 (ttm-80)
REVERT: A  222 PHE cc_start: 0.6027 (t80) cc_final: 0.5553 (t80)
REVERT: A  255 MET cc_start: 0.1089 (mmm) cc_final: -0.1038 (mtp)
REVERT: A  318 TYR cc_start: 0.7857 (t80) cc_final: 0.7613 (t80)
REVERT: A  333 ARG cc_start: 0.8935 (mtp-110) cc_final: 0.8707 (mtp-110)
REVERT: A  338 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8289 (ttmt)
REVERT: A  339 TYR cc_start: 0.8737 (m-80) cc_final: 0.8059 (m-80)
REVERT: B  124 TYR cc_start: 0.8999 (m-80) cc_final: 0.8765 (m-80)
REVERT: B  197 ARG cc_start: 0.7890 (tpp80) cc_final: 0.7198 (tpp80)
REVERT: B  228 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7498 (m-30)
REVERT: B  243 THR cc_start: 0.8683 (p) cc_final: 0.8369 (p)
REVERT: B  262 MET cc_start: 0.8408 (tpp) cc_final: 0.8051 (tpp)
REVERT: B  297 TRP cc_start: 0.9170 (m100) cc_final: 0.8830 (m100)
REVERT: B  325 MET cc_start: 0.8902 (tpp) cc_final: 0.8463 (mmm)
REVERT: G   29 LYS cc_start: 0.8490 (tppt) cc_final: 0.7963 (tptt)
REVERT: N   87 LYS cc_start: 0.7657 (mttt) cc_final: 0.7402 (mmtm)
REVERT: N   95 TYR cc_start: 0.9061 (m-80) cc_final: 0.8523 (m-80)
REVERT: R   81 LYS cc_start: 0.8550 (tptt) cc_final: 0.8187 (tptt)
REVERT: R  125 ILE cc_start: 0.8530 (mm) cc_final: 0.7850 (mt)
REVERT: R  142 ILE cc_start: 0.7797 (mt) cc_final: 0.7461 (mt)
REVERT: R  154 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8277 (mt)
REVERT: R  163 TRP cc_start: 0.6086 (m100) cc_final: 0.5796 (m100)
  outliers start: 38
  outliers final: 26
  residues processed: 220
  average time/residue: 0.0997
  time to fit residues: 29.3914
Evaluate side-chains
  211 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 182
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   60 ASN
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  200 VAL
Chi-restraints excluded: chain R residue  202 SER
Chi-restraints excluded: chain R residue  207 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 48 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 56 optimal weight:    0.5980
   chunk 47 optimal weight:    0.0030
   chunk 16 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.5790

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
B  32 GLN
R  60 ASN
** R 323 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 = 0.4062 r_free = 0.4062 target = 0.181748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.147719 restraints weight = 9305.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3700 rms_B_bonded: 2.09
r_work: 0.3567 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.3940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8308  Z= 0.152
  Angle     :  0.573   9.536  11278  Z= 0.297
  Chirality :  0.043   0.155   1282
  Planarity :  0.004   0.051   1422
  Dihedral  :  4.799  54.621   1213
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 17.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 22.79 %
    Favored  : 73.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.27), residues: 1017
  helix:  0.57 (0.26), residues: 401
  sheet: -1.83 (0.37), residues: 179
  loop : -1.10 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 347 
 TYR   0.021   0.001   TYR B 289 
 PHE   0.042   0.002   PHE A 363 
 TRP   0.015   0.002   TRP A 281 
 HIS   0.006   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 8304)
  covalent geometry    : angle       0.57238 (11270)
  SS BOND              : bond        0.00162 (    4)
  SS BOND              : angle       0.89184 (    8)
  hydrogen bonds       : bond        0.03924 (  412)
  hydrogen bonds       : angle       5.27406 ( 1167)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 189
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8294 (tppt) cc_final: 0.7897 (mmtm)
REVERT: A   20 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7353 (ttm-80)
REVERT: A  208 PHE cc_start: 0.4726 (t80) cc_final: 0.3584 (t80)
REVERT: A  222 PHE cc_start: 0.6044 (t80) cc_final: 0.5408 (t80)
REVERT: A  255 MET cc_start: 0.0991 (mmm) cc_final: -0.0979 (mtp)
REVERT: A  292 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.8197 (m-40)
REVERT: A  333 ARG cc_start: 0.8938 (mtp-110) cc_final: 0.8712 (mtp-110)
REVERT: A  338 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8239 (ttmt)
REVERT: A  339 TYR cc_start: 0.8617 (m-80) cc_final: 0.7935 (m-80)
REVERT: B  197 ARG cc_start: 0.7605 (tpp80) cc_final: 0.7058 (tpp80)
REVERT: B  243 THR cc_start: 0.8704 (p) cc_final: 0.8378 (p)
REVERT: B  262 MET cc_start: 0.8422 (tpp) cc_final: 0.8047 (tpp)
REVERT: B  297 TRP cc_start: 0.9172 (m100) cc_final: 0.8891 (m100)
REVERT: B  323 ASP cc_start: 0.8072 (p0) cc_final: 0.7627 (p0)
REVERT: G   29 LYS cc_start: 0.8453 (tppt) cc_final: 0.7946 (tptt)
REVERT: N   80 TYR cc_start: 0.8477 (m-80) cc_final: 0.8120 (m-80)
REVERT: N   87 LYS cc_start: 0.7659 (mttt) cc_final: 0.7442 (mmtm)
REVERT: N   95 TYR cc_start: 0.9045 (m-80) cc_final: 0.8542 (m-80)
REVERT: R   60 ASN cc_start: 0.8993 (OUTLIER) cc_final: 0.8670 (t0)
REVERT: R   81 LYS cc_start: 0.8512 (tptt) cc_final: 0.8065 (tptt)
REVERT: R  125 ILE cc_start: 0.8460 (mm) cc_final: 0.7730 (mt)
REVERT: R  142 ILE cc_start: 0.7799 (mt) cc_final: 0.7428 (mt)
REVERT: R  163 TRP cc_start: 0.6191 (m100) cc_final: 0.5944 (m100)
  outliers start: 33
  outliers final: 22
  residues processed: 210
  average time/residue: 0.0954
  time to fit residues: 27.2605
Evaluate side-chains
  203 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 178
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   60 ASN
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  202 SER
Chi-restraints excluded: chain R residue  207 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 60 optimal weight:    8.9990
   chunk 74 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 83 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
R  60 ASN
** R 323 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 = 0.4048 r_free = 0.4048 target = 0.180575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.145810 restraints weight = 9415.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.12
r_work: 0.3545 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3393 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.4071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8308  Z= 0.174
  Angle     :  0.597   8.365  11278  Z= 0.305
  Chirality :  0.043   0.152   1282
  Planarity :  0.004   0.051   1422
  Dihedral  :  4.835  53.899   1213
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 18.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 23.26 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.26), residues: 1017
  helix:  0.60 (0.26), residues: 401
  sheet: -1.81 (0.37), residues: 180
  loop : -1.14 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 347 
 TYR   0.012   0.002   TYR R 214 
 PHE   0.038   0.002   PHE A 363 
 TRP   0.013   0.002   TRP A 234 
 HIS   0.007   0.002   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 8304)
  covalent geometry    : angle       0.59696 (11270)
  SS BOND              : bond        0.00197 (    4)
  SS BOND              : angle       0.98454 (    8)
  hydrogen bonds       : bond        0.04020 (  412)
  hydrogen bonds       : angle       5.30046 ( 1167)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 183
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8257 (tppt) cc_final: 0.7882 (mmtm)
REVERT: A   20 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7306 (ttm-80)
REVERT: A  208 PHE cc_start: 0.4751 (t80) cc_final: 0.3932 (t80)
REVERT: A  222 PHE cc_start: 0.6035 (t80) cc_final: 0.5531 (t80)
REVERT: A  255 MET cc_start: 0.0967 (mmm) cc_final: -0.0973 (mtp)
REVERT: A  292 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8195 (m-40)
REVERT: A  333 ARG cc_start: 0.8951 (mtp-110) cc_final: 0.8713 (mtp-110)
REVERT: A  338 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8212 (ttmt)
REVERT: B  197 ARG cc_start: 0.7622 (tpp80) cc_final: 0.7059 (tpp80)
REVERT: B  243 THR cc_start: 0.8728 (p) cc_final: 0.8391 (p)
REVERT: B  262 MET cc_start: 0.8356 (tpp) cc_final: 0.8048 (tpp)
REVERT: B  297 TRP cc_start: 0.9166 (m100) cc_final: 0.8963 (m100)
REVERT: G   29 LYS cc_start: 0.8468 (tppt) cc_final: 0.7922 (tptt)
REVERT: N   80 TYR cc_start: 0.8472 (m-80) cc_final: 0.8105 (m-80)
REVERT: N   87 LYS cc_start: 0.7735 (mttt) cc_final: 0.7487 (mmtm)
REVERT: N   95 TYR cc_start: 0.9042 (m-80) cc_final: 0.8557 (m-80)
REVERT: R   81 LYS cc_start: 0.8501 (tptt) cc_final: 0.8113 (tptt)
REVERT: R  125 ILE cc_start: 0.8496 (mm) cc_final: 0.7821 (mt)
REVERT: R  142 ILE cc_start: 0.7822 (mt) cc_final: 0.7445 (mt)
REVERT: R  163 TRP cc_start: 0.6153 (m100) cc_final: 0.5899 (m100)
  outliers start: 32
  outliers final: 24
  residues processed: 201
  average time/residue: 0.0843
  time to fit residues: 23.1218
Evaluate side-chains
  208 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 182
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   60 ASN
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  200 VAL
Chi-restraints excluded: chain R residue  202 SER
Chi-restraints excluded: chain R residue  207 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 32 optimal weight:    0.0980
   chunk 20 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 96 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.181317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.146850 restraints weight = 9301.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 2.12
r_work: 0.3561 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3405 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.4175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8308  Z= 0.154
  Angle     :  0.587   8.246  11278  Z= 0.300
  Chirality :  0.043   0.153   1282
  Planarity :  0.004   0.051   1422
  Dihedral  :  4.821  54.300   1213
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 17.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 23.60 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.27), residues: 1017
  helix:  0.58 (0.26), residues: 407
  sheet: -1.74 (0.37), residues: 179
  loop : -1.19 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 347 
 TYR   0.010   0.001   TYR B  59 
 PHE   0.034   0.002   PHE A 363 
 TRP   0.014   0.002   TRP A 281 
 HIS   0.006   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8304)
  covalent geometry    : angle       0.58666 (11270)
  SS BOND              : bond        0.00155 (    4)
  SS BOND              : angle       0.89862 (    8)
  hydrogen bonds       : bond        0.03913 (  412)
  hydrogen bonds       : angle       5.26872 ( 1167)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 186
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8214 (tppt) cc_final: 0.7818 (mmtm)
REVERT: A   20 ARG cc_start: 0.7595 (ttp80) cc_final: 0.7332 (ttm-80)
REVERT: A  208 PHE cc_start: 0.4774 (OUTLIER) cc_final: 0.4080 (t80)
REVERT: A  222 PHE cc_start: 0.5959 (t80) cc_final: 0.5504 (t80)
REVERT: A  255 MET cc_start: 0.1067 (mmm) cc_final: -0.0870 (mtp)
REVERT: A  265 ARG cc_start: 0.8114 (ttt90) cc_final: 0.7686 (ttm170)
REVERT: A  292 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8237 (m-40)
REVERT: A  333 ARG cc_start: 0.8939 (mtp-110) cc_final: 0.8706 (mtp-110)
REVERT: A  338 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8136 (ttmt)
REVERT: B  197 ARG cc_start: 0.7558 (tpp80) cc_final: 0.7026 (tpp80)
REVERT: B  243 THR cc_start: 0.8703 (p) cc_final: 0.8370 (p)
REVERT: B  262 MET cc_start: 0.8303 (tpp) cc_final: 0.8025 (tpp)
REVERT: B  297 TRP cc_start: 0.9170 (m100) cc_final: 0.8962 (m100)
REVERT: B  323 ASP cc_start: 0.7987 (p0) cc_final: 0.7552 (p0)
REVERT: G   29 LYS cc_start: 0.8462 (tppt) cc_final: 0.7898 (tptt)
REVERT: N   33 LYS cc_start: 0.8671 (ttmt) cc_final: 0.7949 (tttm)
REVERT: N   80 TYR cc_start: 0.8449 (m-80) cc_final: 0.8087 (m-80)
REVERT: N   87 LYS cc_start: 0.7704 (mttt) cc_final: 0.7475 (mmtm)
REVERT: N   95 TYR cc_start: 0.9045 (m-80) cc_final: 0.8582 (m-80)
REVERT: R   81 LYS cc_start: 0.8481 (tptt) cc_final: 0.8091 (tptt)
REVERT: R  105 MET cc_start: 0.8607 (tmm) cc_final: 0.8349 (ttp)
REVERT: R  125 ILE cc_start: 0.8476 (mm) cc_final: 0.7776 (mt)
REVERT: R  142 ILE cc_start: 0.7816 (mt) cc_final: 0.7445 (mt)
REVERT: R  163 TRP cc_start: 0.6108 (m100) cc_final: 0.5851 (m100)
  outliers start: 29
  outliers final: 24
  residues processed: 203
  average time/residue: 0.0929
  time to fit residues: 25.5693
Evaluate side-chains
  209 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 182
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  338 LYS
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  200 VAL
Chi-restraints excluded: chain R residue  202 SER
Chi-restraints excluded: chain R residue  207 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   chunk 24 optimal weight:    9.9990
   chunk 80 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0030
   chunk 47 optimal weight:    3.9990
   chunk 100 optimal weight:    0.7980
   chunk 94 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 32 optimal weight:    0.3980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 224 GLN
** R 323 ASN ** 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 = 0.4059 r_free = 0.4059 target = 0.181479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.146900 restraints weight = 9329.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 2.13
r_work: 0.3559 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3405 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.4193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.183   8308  Z= 0.226
  Angle     :  0.948  59.199  11278  Z= 0.560
  Chirality :  0.044   0.288   1282
  Planarity :  0.004   0.051   1422
  Dihedral  :  4.852  54.297   1213
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 19.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 24.07 %
    Favored  : 72.56 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.27), residues: 1017
  helix:  0.60 (0.26), residues: 407
  sheet: -1.73 (0.37), residues: 179
  loop : -1.20 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 385 
 TYR   0.030   0.002   TYR R 214 
 PHE   0.035   0.002   PHE A 363 
 TRP   0.014   0.002   TRP A 281 
 HIS   0.009   0.002   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 8304)
  covalent geometry    : angle       0.94758 (11270)
  SS BOND              : bond        0.00162 (    4)
  SS BOND              : angle       0.89199 (    8)
  hydrogen bonds       : bond        0.03981 (  412)
  hydrogen bonds       : angle       5.28248 ( 1167)

===============================================================================
Job complete
usr+sys time: 2405.69 seconds
wall clock time: 41 minutes 58.99 seconds (2518.99 seconds total)