Starting phenix.real_space_refine
on Wed Mar 12 11:45:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jr9_36593/03_2025/8jr9_36593_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jr9_36593/03_2025/8jr9_36593.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jr9_36593/03_2025/8jr9_36593.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jr9_36593/03_2025/8jr9_36593.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jr9_36593/03_2025/8jr9_36593_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jr9_36593/03_2025/8jr9_36593_neut_trim.cif"
  }
  resolution = 2.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    5027      2.51       5
     N    1346      2.21       5
     O    1469      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Residue "B ASP  186": not complete - not flipped  Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7893
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1917
          Classifications: {'peptide': 233}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 227}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "B"
      Number of atoms: 2547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2547
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 83
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 7, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 47
    Chain: "G"
      Number of atoms: 389
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 389
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "N"
      Number of atoms: 969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 969
          Classifications: {'peptide': 129}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "R"
      Number of atoms: 2027
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 2027
          Classifications: {'peptide': 255}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 250}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 73
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 68
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 6, 'TRP:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 56
    Chain: "R"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'KHF': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.28, per 1000 atoms: 0.67
  Number of scatterers: 7893
  At special positions: 0
  Unit cell: (92.288, 108.768, 106.296, 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)
     S      48     16.00
     F       3      9.00
     O    1469      8.00
     N    1346      7.00
     C    5027      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 281 " - pdb=" SG  CYS R 351 " distance=2.10

  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: 2.04
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1908

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      42.7% alpha, 21.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 33
      removed outlier: 4.007A  pdb=" N   GLN A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   THR A  33 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 54 through 57
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.558A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 312 through 316
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.833A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.517A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 22
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 4.033A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 108 through 112
      removed outlier: 4.495A  pdb=" N   THR N 111 " --> pdb=" O   PHE N 108 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   SER N 112 " --> pdb=" O   ASP N 109 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 108 through 112'
    Processing helix  chain 'R' and resid 186 through 212
      removed outlier: 3.566A  pdb=" N   PHE R 212 " --> pdb=" O   ILE R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 213 through 216
    Processing helix  chain 'R' and resid 217 through 243
    Processing helix  chain 'R' and resid 278 through 312
      removed outlier: 3.624A  pdb=" N   ASN R 295 " --> pdb=" O   PHE R 291 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   TYR R 296 " --> pdb=" O   LEU R 292 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 316 through 347
      Proline residue:  R 332  - end of helix
    Processing helix  chain 'R' and resid 356 through 359
    Processing helix  chain 'R' and resid 360 through 393
      Proline residue:  R 366  - end of helix
    Processing helix  chain 'R' and resid 400 through 414
    Processing helix  chain 'R' and resid 415 through 427
      removed outlier: 4.366A  pdb=" N   VAL R 419 " --> pdb=" O   PRO R 415 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 437 through 460
      removed outlier: 4.914A  pdb=" N   GLY R 452 " --> pdb=" O   ASN R 448 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   PHE R 453 " --> pdb=" O   SER R 449 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 463 through 481
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.441A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   GLY A  40 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.667A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.649A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.599A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 6.611A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.524A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.981A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.778A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.657A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.825A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.878A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.010A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.582A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.577A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  25 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 5.929A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    416 hydrogen bonds defined for protein.
    1191 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.17

  Time building geometry restraints manager: 2.37 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1286
        1.30 -     1.43: 2203
        1.43 -     1.56: 4509
        1.56 -     1.68: 1
        1.68 -     1.81: 65
  Bond restraints: 8064
  Sorted by residual:
  bond pdb=" C16 KHF R 601 "
       pdb=" N2  KHF R 601 "
    ideal  model  delta    sigma   weight residual
    1.274  1.458 -0.184 2.00e-02 2.50e+03 8.46e+01
  bond pdb=" C25 KHF R 601 "
       pdb=" N4  KHF R 601 "
    ideal  model  delta    sigma   weight residual
    1.353  1.455 -0.102 2.00e-02 2.50e+03 2.60e+01
  bond pdb=" C12 KHF R 601 "
       pdb=" C13 KHF R 601 "
    ideal  model  delta    sigma   weight residual
    1.530  1.429  0.101 2.00e-02 2.50e+03 2.53e+01
  bond pdb=" C13 KHF R 601 "
       pdb=" C14 KHF R 601 "
    ideal  model  delta    sigma   weight residual
    1.532  1.440  0.092 2.00e-02 2.50e+03 2.13e+01
  bond pdb=" C   TYR B 145 "
       pdb=" N   LEU B 146 "
    ideal  model  delta    sigma   weight residual
    1.331  1.275  0.055 1.41e-02 5.03e+03 1.54e+01
  ... (remaining 8059 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.44: 10934
        4.44 -     8.88: 21
        8.88 -    13.32: 1
       13.32 -    17.76: 1
       17.76 -    22.20: 2
  Bond angle restraints: 10959
  Sorted by residual:
  angle pdb=" C12 KHF R 601 "
        pdb=" C13 KHF R 601 "
        pdb=" N2  KHF R 601 "
      ideal   model   delta    sigma   weight residual
     110.89  133.09  -22.20 3.00e+00 1.11e-01 5.48e+01
  angle pdb=" C14 KHF R 601 "
        pdb=" C13 KHF R 601 "
        pdb=" N2  KHF R 601 "
      ideal   model   delta    sigma   weight residual
     110.23   90.48   19.75 3.00e+00 1.11e-01 4.33e+01
  angle pdb=" O1  KHF R 601 "
        pdb=" S1  KHF R 601 "
        pdb=" O2  KHF R 601 "
      ideal   model   delta    sigma   weight residual
     118.72  101.40   17.32 3.00e+00 1.11e-01 3.33e+01
  angle pdb=" O   TYR B 145 "
        pdb=" C   TYR B 145 "
        pdb=" N   LEU B 146 "
      ideal   model   delta    sigma   weight residual
     122.89  116.90    5.99 1.22e+00 6.72e-01 2.41e+01
  angle pdb=" N   GLN A 294 "
        pdb=" CA  GLN A 294 "
        pdb=" C   GLN A 294 "
      ideal   model   delta    sigma   weight residual
     113.23  107.35    5.88 1.24e+00 6.50e-01 2.25e+01
  ... (remaining 10954 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.08: 4361
       25.08 -    50.15: 344
       50.15 -    75.23: 38
       75.23 -   100.31: 2
      100.31 -   125.39: 10
  Dihedral angle restraints: 4755
    sinusoidal: 1805
      harmonic: 2950
  Sorted by residual:
  dihedral pdb=" CA  ASP B 186 "
           pdb=" CB  ASP B 186 "
           pdb=" CG  ASP B 186 "
           pdb=" OD1 ASP B 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
      70.00  175.51 -105.51     1      2.00e+01 2.50e-03 3.04e+01
  dihedral pdb=" C25 KHF R 601 "
           pdb=" C27 KHF R 601 "
           pdb=" N4  KHF R 601 "
           pdb=" C29 KHF R 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     116.77 -117.84 -125.39     1      3.00e+01 1.11e-03 1.68e+01
  dihedral pdb=" C28 KHF R 601 "
           pdb=" C27 KHF R 601 "
           pdb=" N4  KHF R 601 "
           pdb=" C4  KHF R 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.48   60.62 -125.10     1      3.00e+01 1.11e-03 1.68e+01
  ... (remaining 4752 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 993
       0.045 -    0.090: 181
       0.090 -    0.135: 57
       0.135 -    0.180: 2
       0.180 -    0.225: 4
  Chirality restraints: 1237
  Sorted by residual:
  chirality pdb=" CA  LEU B 190 "
            pdb=" N   LEU B 190 "
            pdb=" C   LEU B 190 "
            pdb=" CB  LEU B 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  VAL R 243 "
            pdb=" N   VAL R 243 "
            pdb=" C   VAL R 243 "
            pdb=" CB  VAL R 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1234 not shown)

  Planarity restraints: 1387
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  87 "    0.009 2.00e-02 2.50e+03   1.71e-02 2.91e+00
        pdb=" C   THR B  87 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   THR B  87 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ASN B  88 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 331 "    0.027 5.00e-02 4.00e+02   4.12e-02 2.72e+00
        pdb=" N   PRO A 332 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 332 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 332 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 145 "    0.007 2.00e-02 2.50e+03   1.30e-02 1.70e+00
        pdb=" C   TYR B 145 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   TYR B 145 "    0.008 2.00e-02 2.50e+03
        pdb=" N   LEU B 146 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1384 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1471
        2.77 -     3.30: 7376
        3.30 -     3.84: 13547
        3.84 -     4.37: 15152
        4.37 -     4.90: 26951
  Nonbonded interactions: 64497
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   LEU B  30 "
            pdb=" OG1 THR B  34 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   VAL R 423 "
            pdb=" OG1 THR R 427 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   THR A 325 "
            pdb=" OG1 THR A 325 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OG  SER B  97 "
            pdb=" OD2 ASP B 118 "
     model   vdw
     2.305 3.040
  ... (remaining 64492 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:             1.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     22.210
  Find NCS groups from input model:        0.070
  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:21.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.184   8064  Z= 0.324
  Angle     :  0.649  22.198  10959  Z= 0.337
  Chirality :  0.040   0.225   1237
  Planarity :  0.003   0.041   1387
  Dihedral  : 17.649 125.387   2838
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 24.85 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.27), residues: 994
  helix:  2.79 (0.26), residues: 400
  sheet:  0.86 (0.36), residues: 206
  loop : -0.32 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 234 
 HIS   0.004   0.000   HIS A 387 
 PHE   0.014   0.001   PHE R 238 
 TYR   0.009   0.001   TYR R 191 
 ARG   0.007   0.000   ARG A  15 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 197
  time to evaluate  : 0.871 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6317 (pp20)
REVERT: A   15 ARG cc_start: 0.6178 (ttt-90) cc_final: 0.5290 (ttm110)
REVERT: A   21 LYS cc_start: 0.7531 (mtpt) cc_final: 0.6548 (tptp)
REVERT: A  213 GLN cc_start: 0.7928 (mt0) cc_final: 0.7427 (tt0)
REVERT: A  221 MET cc_start: 0.7744 (ptp) cc_final: 0.7421 (ttp)
REVERT: A  240 ASP cc_start: 0.5941 (p0) cc_final: 0.5720 (p0)
REVERT: A  268 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6501 (tp30)
REVERT: A  347 ARG cc_start: 0.7238 (ptp90) cc_final: 0.6813 (ptp-170)
REVERT: A  380 ARG cc_start: 0.7733 (ttm110) cc_final: 0.7263 (ttm110)
REVERT: A  389 ARG cc_start: 0.7779 (tpp-160) cc_final: 0.7326 (mtm110)
REVERT: B   90 VAL cc_start: 0.7823 (m) cc_final: 0.7602 (p)
REVERT: B   97 SER cc_start: 0.7018 (p) cc_final: 0.6716 (t)
REVERT: B  155 ASN cc_start: 0.6327 (t0) cc_final: 0.6086 (t0)
REVERT: B  226 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7037 (mt-10)
REVERT: B  325 MET cc_start: 0.8175 (tpp) cc_final: 0.7853 (tpp)
REVERT: N  113 THR cc_start: 0.8213 (p) cc_final: 0.7979 (t)
REVERT: R  189 MET cc_start: 0.6914 (tpt) cc_final: 0.6519 (tpp)
  outliers start: 2
  outliers final: 1
  residues processed: 198
  average time/residue: 1.0160
  time to fit residues: 216.1165
Evaluate side-chains
  126 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  425 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 50 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 77 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 57 optimal weight:   10.0000
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 ASN
B  75 GLN
B 119 ASN
B 176 GLN
B 259 GLN
B 295 ASN
G  44 HIS
N   5 GLN
N  35 ASN
** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 467 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.190094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.154978 restraints weight = 8559.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3768 rms_B_bonded: 1.54
r_work: 0.3665 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3556 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8064  Z= 0.204
  Angle     :  0.530   6.168  10959  Z= 0.284
  Chirality :  0.041   0.135   1237
  Planarity :  0.004   0.037   1387
  Dihedral  : 12.255 126.431   1145
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 21.18 %
    Favored  : 74.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.27), residues: 994
  helix:  3.14 (0.25), residues: 398
  sheet:  1.21 (0.34), residues: 206
  loop : -0.29 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 169 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.015   0.002   PHE A 363 
 TYR   0.018   0.002   TYR A 339 
 ARG   0.005   0.001   ARG A  15 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 143
  time to evaluate  : 0.763 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6876 (pp20)
REVERT: A   15 ARG cc_start: 0.6569 (ttt-90) cc_final: 0.6113 (ttp80)
REVERT: A   21 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7258 (pptt)
REVERT: A   25 LYS cc_start: 0.7620 (ttmm) cc_final: 0.7172 (mttp)
REVERT: A  213 GLN cc_start: 0.8544 (mt0) cc_final: 0.8067 (tt0)
REVERT: A  240 ASP cc_start: 0.6866 (p0) cc_final: 0.6613 (p0)
REVERT: A  299 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6908 (mm-30)
REVERT: A  370 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7353 (mp0)
REVERT: A  389 ARG cc_start: 0.8034 (tpp-160) cc_final: 0.7704 (mtm110)
REVERT: B   97 SER cc_start: 0.7750 (p) cc_final: 0.7479 (t)
REVERT: B  197 ARG cc_start: 0.7268 (tpp-160) cc_final: 0.6638 (mmt90)
REVERT: G   37 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7432 (mt)
REVERT: N   34 MET cc_start: 0.8359 (mmm) cc_final: 0.7859 (mmm)
REVERT: N   70 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8057 (tt)
REVERT: N   73 ASP cc_start: 0.6857 (t70) cc_final: 0.6644 (t70)
REVERT: R  189 MET cc_start: 0.6611 (tpt) cc_final: 0.6206 (tpp)
REVERT: R  410 THR cc_start: 0.8704 (t) cc_final: 0.8445 (m)
  outliers start: 38
  outliers final: 8
  residues processed: 169
  average time/residue: 1.4203
  time to fit residues: 256.6320
Evaluate side-chains
  133 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   70 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 97 optimal weight:    0.4980
   chunk 7 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0020
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.8992

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 264 ASN
A 271 ASN
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
N   5 GLN
** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 364 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.183108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.149458 restraints weight = 8727.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 1.58
r_work: 0.3565 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3455 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.3217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8064  Z= 0.200
  Angle     :  0.517   9.570  10959  Z= 0.276
  Chirality :  0.040   0.140   1237
  Planarity :  0.003   0.043   1387
  Dihedral  : 12.295 127.500   1142
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 21.42 %
    Favored  : 74.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.27), residues: 994
  helix:  3.19 (0.25), residues: 398
  sheet:  1.11 (0.34), residues: 208
  loop : -0.36 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 211 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.011   0.001   PHE A 363 
 TYR   0.014   0.001   TYR A 339 
 ARG   0.007   0.001   ARG B  96 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 137
  time to evaluate  : 0.888 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7002 (pp20)
REVERT: A   21 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7508 (pptt)
REVERT: A   24 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.7139 (mp10)
REVERT: A   25 LYS cc_start: 0.7886 (ttmm) cc_final: 0.7575 (mttp)
REVERT: A   28 GLN cc_start: 0.7589 (mt0) cc_final: 0.7302 (mm-40)
REVERT: A  268 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7439 (tp30)
REVERT: A  347 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7884 (ttp-110)
REVERT: A  389 ARG cc_start: 0.8208 (tpp-160) cc_final: 0.7879 (mtm110)
REVERT: B  170 ASP cc_start: 0.7759 (p0) cc_final: 0.7525 (p0)
REVERT: B  197 ARG cc_start: 0.7354 (tpp-160) cc_final: 0.6804 (mmt90)
REVERT: B  291 ASP cc_start: 0.7619 (p0) cc_final: 0.7407 (p0)
REVERT: N    3 GLN cc_start: 0.7660 (pt0) cc_final: 0.7458 (pt0)
REVERT: R  189 MET cc_start: 0.6679 (tpt) cc_final: 0.6223 (tpp)
REVERT: R  410 THR cc_start: 0.8806 (t) cc_final: 0.8512 (m)
  outliers start: 37
  outliers final: 12
  residues processed: 161
  average time/residue: 1.0887
  time to fit residues: 186.8518
Evaluate side-chains
  133 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain R residue  198 SER
Chi-restraints excluded: chain R residue  224 MET
Chi-restraints excluded: chain R residue  307 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 82 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   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 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 ASN
A 279 ASN
A 390 GLN
B  75 GLN
B 259 GLN
N  31 ASN
** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 364 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.181708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.145438 restraints weight = 8579.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 1.58
r_work: 0.3553 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3444 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.3565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8064  Z= 0.183
  Angle     :  0.505   6.874  10959  Z= 0.269
  Chirality :  0.040   0.149   1237
  Planarity :  0.003   0.045   1387
  Dihedral  : 12.191 127.521   1142
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 21.66 %
    Favored  : 74.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.27), residues: 994
  helix:  3.22 (0.25), residues: 398
  sheet:  1.22 (0.34), residues: 208
  loop : -0.37 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 234 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.011   0.001   PHE R 327 
 TYR   0.015   0.001   TYR R 297 
 ARG   0.007   0.000   ARG B  96 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 122
  time to evaluate  : 0.855 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8147 (mtpt) cc_final: 0.7421 (pptt)
REVERT: A   25 LYS cc_start: 0.8030 (ttmm) cc_final: 0.7678 (mttp)
REVERT: A   28 GLN cc_start: 0.7638 (mt0) cc_final: 0.7256 (mm-40)
REVERT: A  268 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7250 (tp30)
REVERT: A  370 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7524 (pm20)
REVERT: A  389 ARG cc_start: 0.8132 (tpp-160) cc_final: 0.7764 (mtm110)
REVERT: B  197 ARG cc_start: 0.7337 (tpp-160) cc_final: 0.6774 (mmt90)
REVERT: N   20 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7372 (pp)
REVERT: R  189 MET cc_start: 0.6602 (tpt) cc_final: 0.6184 (tpp)
REVERT: R  410 THR cc_start: 0.8815 (t) cc_final: 0.8478 (m)
  outliers start: 35
  outliers final: 18
  residues processed: 148
  average time/residue: 1.1515
  time to fit residues: 181.9501
Evaluate side-chains
  135 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  198 SER
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  307 HIS
Chi-restraints excluded: chain R residue  342 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 87 optimal weight:    0.0070
   chunk 88 optimal weight:    5.9990
   chunk 95 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0870
   chunk 14 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 34 optimal weight:    0.5980
   chunk 80 optimal weight:    0.0570
   overall best weight:    0.3494

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 ASN
A 390 GLN
B 259 GLN
** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 364 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.184715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.149315 restraints weight = 8631.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 1.55
r_work: 0.3616 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3507 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.3630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8064  Z= 0.135
  Angle     :  0.455   6.609  10959  Z= 0.242
  Chirality :  0.039   0.141   1237
  Planarity :  0.003   0.044   1387
  Dihedral  : 11.971 127.285   1142
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 22.03 %
    Favored  : 74.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.26 (0.27), residues: 994
  helix:  3.36 (0.26), residues: 398
  sheet:  1.33 (0.34), residues: 203
  loop : -0.43 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.011   0.001   PHE R 327 
 TYR   0.013   0.001   TYR N  80 
 ARG   0.002   0.000   ARG B 314 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 0.784 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8141 (mtpt) cc_final: 0.7423 (pptt)
REVERT: A   25 LYS cc_start: 0.7939 (ttmm) cc_final: 0.7608 (mttp)
REVERT: A   28 GLN cc_start: 0.7643 (mt0) cc_final: 0.7257 (mm-40)
REVERT: A   55 ILE cc_start: 0.6113 (OUTLIER) cc_final: 0.5721 (pp)
REVERT: A  268 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7294 (tp30)
REVERT: A  299 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7060 (mm-30)
REVERT: A  389 ARG cc_start: 0.8064 (tpp-160) cc_final: 0.7722 (mtm110)
REVERT: B  196 THR cc_start: 0.7410 (OUTLIER) cc_final: 0.7205 (p)
REVERT: B  197 ARG cc_start: 0.7170 (tpp-160) cc_final: 0.6598 (mmt90)
REVERT: R  189 MET cc_start: 0.6609 (tpt) cc_final: 0.6184 (tpp)
REVERT: R  410 THR cc_start: 0.8752 (t) cc_final: 0.8448 (m)
REVERT: R  414 MET cc_start: 0.7230 (ptt) cc_final: 0.6716 (ttm)
  outliers start: 29
  outliers final: 14
  residues processed: 151
  average time/residue: 1.1128
  time to fit residues: 179.0007
Evaluate side-chains
  129 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   52 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  307 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 264 ASN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 364 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.177870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.143819 restraints weight = 8569.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 1.50
r_work: 0.3502 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3392 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.4286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8064  Z= 0.334
  Angle     :  0.607   7.175  10959  Z= 0.326
  Chirality :  0.044   0.151   1237
  Planarity :  0.004   0.048   1387
  Dihedral  : 12.286 128.112   1142
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 20.56 %
    Favored  : 74.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.27), residues: 994
  helix:  2.96 (0.25), residues: 397
  sheet:  1.06 (0.34), residues: 205
  loop : -0.48 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 234 
 HIS   0.009   0.002   HIS A 357 
 PHE   0.014   0.002   PHE R 327 
 TYR   0.021   0.002   TYR R 297 
 ARG   0.004   0.001   ARG A 385 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 122
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7432 (tptp)
REVERT: A   28 GLN cc_start: 0.7779 (mt0) cc_final: 0.7357 (mp10)
REVERT: A   55 ILE cc_start: 0.6213 (OUTLIER) cc_final: 0.5847 (pp)
REVERT: A  220 HIS cc_start: 0.8482 (m170) cc_final: 0.8234 (m-70)
REVERT: A  268 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7429 (tt0)
REVERT: A  374 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8357 (mtt180)
REVERT: A  389 ARG cc_start: 0.8123 (tpp-160) cc_final: 0.7840 (mtm110)
REVERT: B   65 THR cc_start: 0.8036 (m) cc_final: 0.7777 (p)
REVERT: B  142 HIS cc_start: 0.8779 (OUTLIER) cc_final: 0.8507 (m170)
REVERT: B  146 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8643 (mm)
REVERT: B  196 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.7383 (p)
REVERT: B  197 ARG cc_start: 0.7354 (tpp-160) cc_final: 0.6789 (mmt90)
REVERT: B  314 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8293 (ptt180)
REVERT: N   20 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7599 (pp)
REVERT: R  189 MET cc_start: 0.6655 (tpt) cc_final: 0.6227 (tpp)
REVERT: R  199 LEU cc_start: 0.7940 (tp) cc_final: 0.7724 (tt)
  outliers start: 41
  outliers final: 15
  residues processed: 153
  average time/residue: 1.4694
  time to fit residues: 238.5701
Evaluate side-chains
  135 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain A residue  374 ARG
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  307 HIS
Chi-restraints excluded: chain R residue  326 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 59 optimal weight:    8.9990
   chunk 70 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0870
   chunk 16 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 390 GLN
B 259 GLN
R 295 ASN
** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 364 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.181731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.145917 restraints weight = 8532.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 1.54
r_work: 0.3558 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3446 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.4201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8064  Z= 0.167
  Angle     :  0.500   6.392  10959  Z= 0.267
  Chirality :  0.039   0.145   1237
  Planarity :  0.003   0.047   1387
  Dihedral  : 11.936 127.467   1142
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 22.28 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.27), residues: 994
  helix:  3.18 (0.26), residues: 397
  sheet:  1.25 (0.34), residues: 206
  loop : -0.47 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.011   0.001   PHE R 327 
 TYR   0.013   0.001   TYR R 297 
 ARG   0.004   0.000   ARG B  96 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.849 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8271 (mtpt) cc_final: 0.7797 (mptt)
REVERT: A   28 GLN cc_start: 0.7771 (mt0) cc_final: 0.7295 (mp10)
REVERT: A   55 ILE cc_start: 0.6228 (OUTLIER) cc_final: 0.5944 (pt)
REVERT: A  268 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7335 (tp30)
REVERT: A  389 ARG cc_start: 0.8070 (tpp-160) cc_final: 0.7739 (mtm110)
REVERT: B   65 THR cc_start: 0.7955 (m) cc_final: 0.7691 (p)
REVERT: B  197 ARG cc_start: 0.7310 (tpp-160) cc_final: 0.6741 (mmt90)
REVERT: N   20 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7493 (pp)
REVERT: R  189 MET cc_start: 0.6581 (tpt) cc_final: 0.6141 (tpp)
  outliers start: 24
  outliers final: 15
  residues processed: 138
  average time/residue: 1.1015
  time to fit residues: 162.3243
Evaluate side-chains
  130 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  224 MET
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  307 HIS
Chi-restraints excluded: chain R residue  342 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 79 optimal weight:    0.7980
   chunk 93 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 67 optimal weight:    0.7980
   chunk 59 optimal weight:    8.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 364 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.181423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.145397 restraints weight = 8573.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 1.54
r_work: 0.3563 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3452 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.4262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8064  Z= 0.187
  Angle     :  0.510   6.466  10959  Z= 0.272
  Chirality :  0.040   0.150   1237
  Planarity :  0.003   0.047   1387
  Dihedral  : 11.830 127.431   1142
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 22.15 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.27), residues: 994
  helix:  3.17 (0.26), residues: 397
  sheet:  1.16 (0.34), residues: 208
  loop : -0.42 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.012   0.001   PHE R 327 
 TYR   0.014   0.001   TYR R 297 
 ARG   0.004   0.000   ARG B  96 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.836 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7763 (mptt)
REVERT: A   28 GLN cc_start: 0.7789 (mt0) cc_final: 0.7302 (mp10)
REVERT: A   55 ILE cc_start: 0.6235 (OUTLIER) cc_final: 0.5947 (pt)
REVERT: A  389 ARG cc_start: 0.8086 (tpp-160) cc_final: 0.7788 (mtm110)
REVERT: B   65 THR cc_start: 0.7962 (m) cc_final: 0.7703 (p)
REVERT: B  197 ARG cc_start: 0.7220 (tpp-160) cc_final: 0.6632 (mmt90)
REVERT: B  314 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8129 (ptt180)
REVERT: N   20 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7494 (pp)
REVERT: R  189 MET cc_start: 0.6614 (tpt) cc_final: 0.6188 (tpp)
  outliers start: 25
  outliers final: 14
  residues processed: 135
  average time/residue: 1.1201
  time to fit residues: 160.8278
Evaluate side-chains
  133 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  224 MET
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  307 HIS
Chi-restraints excluded: chain R residue  342 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 80 optimal weight:    9.9990
   chunk 8 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
** R 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 364 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.181741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.145871 restraints weight = 8664.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 1.54
r_work: 0.3568 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3455 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.4315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8064  Z= 0.180
  Angle     :  0.509   6.457  10959  Z= 0.270
  Chirality :  0.041   0.163   1237
  Planarity :  0.003   0.047   1387
  Dihedral  : 11.553 127.405   1142
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 23.13 %
    Favored  : 74.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.27), residues: 994
  helix:  3.17 (0.26), residues: 397
  sheet:  1.14 (0.34), residues: 208
  loop : -0.38 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.012   0.001   PHE R 327 
 TYR   0.014   0.001   TYR R 297 
 ARG   0.004   0.000   ARG B  96 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.860 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8262 (mtpt) cc_final: 0.7793 (mptt)
REVERT: A   28 GLN cc_start: 0.7807 (mt0) cc_final: 0.7306 (mp10)
REVERT: A   55 ILE cc_start: 0.6299 (OUTLIER) cc_final: 0.6031 (pt)
REVERT: A  389 ARG cc_start: 0.8035 (tpp-160) cc_final: 0.7737 (mtm110)
REVERT: B   65 THR cc_start: 0.7933 (m) cc_final: 0.7683 (p)
REVERT: B  197 ARG cc_start: 0.7315 (tpp-160) cc_final: 0.6710 (mmt90)
REVERT: B  314 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8129 (ptt180)
REVERT: N   20 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7500 (pp)
REVERT: R  189 MET cc_start: 0.6568 (tpt) cc_final: 0.6131 (tpp)
  outliers start: 18
  outliers final: 13
  residues processed: 131
  average time/residue: 1.1459
  time to fit residues: 159.5718
Evaluate side-chains
  128 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue  224 MET
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  307 HIS
Chi-restraints excluded: chain R residue  342 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   chunk 86 optimal weight:    0.6980
   chunk 89 optimal weight:    3.9990
   chunk 76 optimal weight:    0.3980
   chunk 17 optimal weight:    0.3980
   chunk 8 optimal weight:    0.0570
   chunk 38 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B 259 GLN
R 295 ASN
** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 364 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.183485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.147791 restraints weight = 8613.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 1.54
r_work: 0.3596 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3487 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.4281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8064  Z= 0.152
  Angle     :  0.488   6.844  10959  Z= 0.258
  Chirality :  0.040   0.157   1237
  Planarity :  0.003   0.047   1387
  Dihedral  : 11.286 127.228   1142
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 23.13 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.27), residues: 994
  helix:  3.26 (0.26), residues: 396
  sheet:  1.10 (0.35), residues: 207
  loop : -0.35 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.011   0.001   PHE R 327 
 TYR   0.012   0.001   TYR R 297 
 ARG   0.004   0.000   ARG B  96 

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

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

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1988 Ramachandran restraints generated.
    994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.805 
Fit side-chains
REVERT: A   21 LYS cc_start: 0.8252 (mtpt) cc_final: 0.7802 (mptt)
REVERT: A   28 GLN cc_start: 0.7781 (mt0) cc_final: 0.7316 (mp10)
REVERT: A   55 ILE cc_start: 0.6312 (OUTLIER) cc_final: 0.6064 (pt)
REVERT: A  389 ARG cc_start: 0.8028 (tpp-160) cc_final: 0.7731 (mtm110)
REVERT: B  197 ARG cc_start: 0.7323 (tpp-160) cc_final: 0.6717 (mmt90)
REVERT: N   20 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7458 (pp)
REVERT: R  189 MET cc_start: 0.6593 (tpt) cc_final: 0.6196 (tpp)
REVERT: R  414 MET cc_start: 0.7199 (ptt) cc_final: 0.6782 (ttm)
  outliers start: 16
  outliers final: 11
  residues processed: 129
  average time/residue: 1.1423
  time to fit residues: 156.5964
Evaluate side-chains
  128 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  335 THR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain R residue  224 MET
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  307 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 63 optimal weight:    0.4980
   chunk 5 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 93 optimal weight:    0.7980
   chunk 36 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.181817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.145855 restraints weight = 8529.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 1.53
r_work: 0.3554 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3442 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.4374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8064  Z= 0.185
  Angle     :  0.511   6.860  10959  Z= 0.271
  Chirality :  0.041   0.160   1237
  Planarity :  0.003   0.047   1387
  Dihedral  : 11.267 127.414   1142
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 23.26 %
    Favored  : 74.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.27), residues: 994
  helix:  3.19 (0.26), residues: 397
  sheet:  1.10 (0.35), residues: 197
  loop : -0.40 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 234 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.012   0.001   PHE R 327 
 TYR   0.019   0.001   TYR N  80 
 ARG   0.004   0.000   ARG B  96 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7064.11 seconds
wall clock time: 124 minutes 20.44 seconds (7460.44 seconds total)