Starting phenix.real_space_refine
on Fri Aug 22 20:31:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gdb_29945/08_2025/8gdb_29945_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gdb_29945/08_2025/8gdb_29945.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gdb_29945/08_2025/8gdb_29945.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gdb_29945/08_2025/8gdb_29945.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gdb_29945/08_2025/8gdb_29945_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gdb_29945/08_2025/8gdb_29945_neut.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    4856      2.51       5
     N    1336      2.21       5
     O    1374      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7612
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1751
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 47}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 169
          Unresolved non-hydrogen angles: 210
          Unresolved non-hydrogen dihedrals: 136
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 8, 'ARG:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 115
    Chain: "B"
      Number of atoms: 2475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2475
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 166
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 11, 'GLN:plan1': 3, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASN%COO:plan1': 1}
          Unresolved non-hydrogen planarities: 105
    Chain: "G"
      Number of atoms: 381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 381
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 36
    Chain: "N"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 904
          Classifications: {'peptide': 126}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "R"
      Number of atoms: 2076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2076
          Classifications: {'peptide': 283}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 12, 'TRANS': 270}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 142
          Unresolved non-hydrogen angles: 172
          Unresolved non-hydrogen dihedrals: 117
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 64
    Chain: "R"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'P2E': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.71, per 1000 atoms: 0.22
  Number of scatterers: 7612
  At special positions: 0
  Unit cell: (99.36, 99.36, 124.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      46     16.00
     O    1374      8.00
     N    1336      7.00
     C    4856      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.45
  Conformation dependent library (CDL) restraints added in 314.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1948

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 11 sheets defined
      40.3% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 39
      removed outlier: 3.781A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 58
      removed outlier: 3.672A  pdb=" N   LYS A  58 " --> pdb=" O   ASN A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 240
      removed outlier: 3.767A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ASP A 240 " --> pdb=" O   CYS A 237 " (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
      removed outlier: 3.672A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 350
      removed outlier: 3.536A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 389
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.605A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.907A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.760A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 21 through 44
      removed outlier: 3.550A  pdb=" N   ALA R  38 " --> pdb=" O   GLY R  34 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE R  39 " --> pdb=" O   ASN R  35 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 46 through 50
      removed outlier: 3.681A  pdb=" N   LYS R  50 " --> pdb=" O   LYS R  47 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 54 through 82
      Proline residue:  R  74  - end of helix
      removed outlier: 3.633A  pdb=" N   ILE R  77 " --> pdb=" O   SER R  73 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 87 through 123
      removed outlier: 4.002A  pdb=" N   LEU R  91 " --> pdb=" O   GLY R  87 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   CYS R  92 " --> pdb=" O   GLY R  88 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   GLU R  93 " --> pdb=" O   GLN R  89 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   TYR R  94 " --> pdb=" O   PRO R  90 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   HIS R 123 " --> pdb=" O   LEU R 119 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 123 through 131
    Processing helix  chain 'R' and resid 132 through 153
      removed outlier: 3.673A  pdb=" N   ALA R 136 " --> pdb=" O   ASP R 132 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 179 through 221
    Processing helix  chain 'R' and resid 267 through 298
      Proline residue:  R 287  - end of helix
    Processing helix  chain 'R' and resid 309 through 330
      Proline residue:  R 322  - end of helix
      Proline residue:  R 326  - end of helix
      removed outlier: 3.984A  pdb=" N   TYR R 329 " --> pdb=" O   ASP R 325 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 333 through 344
      removed outlier: 4.385A  pdb=" N   LYS R 339 " --> pdb=" O   THR R 335 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.832A  pdb=" N   ASP A 223 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.985A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.644A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.717A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.860A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.411A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.928A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.607A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.072A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.186A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.615A  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: 3.531A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.795A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 7
      removed outlier: 3.514A  pdb=" N   SER N  21 " --> pdb=" O   SER N   7 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.790A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 162 through 163

    396 hydrogen bonds defined for protein.
    1155 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: 0.90

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1419
        1.33 -     1.45: 1969
        1.45 -     1.57: 4314
        1.57 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 7764
  Sorted by residual:
  bond pdb=" C1  P2E R 501 "
       pdb=" O2  P2E R 501 "
    ideal  model  delta    sigma   weight residual
    1.250  1.306 -0.056 2.00e-02 2.50e+03 7.70e+00
  bond pdb=" C1  P2E R 501 "
       pdb=" C2  P2E R 501 "
    ideal  model  delta    sigma   weight residual
    1.539  1.499  0.040 2.00e-02 2.50e+03 3.94e+00
  bond pdb=" C1  P2E R 501 "
       pdb=" O1  P2E R 501 "
    ideal  model  delta    sigma   weight residual
    1.247  1.211  0.036 2.00e-02 2.50e+03 3.29e+00
  bond pdb=" C   ILE R 286 "
       pdb=" N   PRO R 287 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.023 1.36e-02 5.41e+03 2.89e+00
  bond pdb=" N   PRO R  24 "
       pdb=" CD  PRO R  24 "
    ideal  model  delta    sigma   weight residual
    1.473  1.495 -0.022 1.40e-02 5.10e+03 2.50e+00
  ... (remaining 7759 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 10119
        1.71 -     3.41: 381
        3.41 -     5.12: 57
        5.12 -     6.82: 20
        6.82 -     8.53: 7
  Bond angle restraints: 10584
  Sorted by residual:
  angle pdb=" C   TYR A 360 "
        pdb=" N   PRO A 361 "
        pdb=" CA  PRO A 361 "
      ideal   model   delta    sigma   weight residual
     119.76  125.82   -6.06 1.00e+00 1.00e+00 3.68e+01
  angle pdb=" N   GLN R  84 "
        pdb=" CA  GLN R  84 "
        pdb=" C   GLN R  84 "
      ideal   model   delta    sigma   weight residual
     109.59  116.44   -6.85 1.47e+00 4.63e-01 2.17e+01
  angle pdb=" N   VAL R  75 "
        pdb=" CA  VAL R  75 "
        pdb=" C   VAL R  75 "
      ideal   model   delta    sigma   weight residual
     110.30  114.06   -3.76 9.70e-01 1.06e+00 1.50e+01
  angle pdb=" C   GLU A 327 "
        pdb=" N   PRO A 328 "
        pdb=" CA  PRO A 328 "
      ideal   model   delta    sigma   weight residual
     118.97  115.28    3.69 1.04e+00 9.25e-01 1.26e+01
  angle pdb=" N   LEU R  71 "
        pdb=" CA  LEU R  71 "
        pdb=" C   LEU R  71 "
      ideal   model   delta    sigma   weight residual
     111.40  115.64   -4.24 1.22e+00 6.72e-01 1.21e+01
  ... (remaining 10579 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.78: 4234
       19.78 -    39.55: 279
       39.55 -    59.33: 36
       59.33 -    79.10: 15
       79.10 -    98.88: 5
  Dihedral angle restraints: 4569
    sinusoidal: 1557
      harmonic: 3012
  Sorted by residual:
  dihedral pdb=" CA  LYS N  33 "
           pdb=" C   LYS N  33 "
           pdb=" N   MET N  34 "
           pdb=" CA  MET N  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.11   29.89     0      5.00e+00 4.00e-02 3.57e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.87   24.13     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  LEU R 331 "
           pdb=" C   LEU R 331 "
           pdb=" N   LEU R 332 "
           pdb=" CA  LEU R 332 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.56   20.44     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 4566 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 848
       0.045 -    0.090: 280
       0.090 -    0.136: 97
       0.136 -    0.181: 17
       0.181 -    0.226: 7
  Chirality restraints: 1249
  Sorted by residual:
  chirality pdb=" CB  VAL R 320 "
            pdb=" CA  VAL R 320 "
            pdb=" CG1 VAL R 320 "
            pdb=" CG2 VAL R 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" C8  P2E R 501 "
            pdb=" C12 P2E R 501 "
            pdb=" C7  P2E R 501 "
            pdb=" C9  P2E R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.75    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  TYR B  59 "
            pdb=" N   TYR B  59 "
            pdb=" C   TYR B  59 "
            pdb=" CB  TYR B  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 1246 not shown)

  Planarity restraints: 1352
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP R 325 "    0.043 5.00e-02 4.00e+02   6.42e-02 6.60e+00
        pdb=" N   PRO R 326 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO R 326 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R 326 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R  23 "   -0.043 5.00e-02 4.00e+02   6.38e-02 6.51e+00
        pdb=" N   PRO R  24 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO R  24 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO R  24 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.041 5.00e-02 4.00e+02   6.25e-02 6.25e+00
        pdb=" N   PRO B 236 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 1349 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1642
        2.78 -     3.31: 6632
        3.31 -     3.84: 12057
        3.84 -     4.37: 13731
        4.37 -     4.90: 25174
  Nonbonded interactions: 59236
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 230 "
            pdb=" NH1 ARG A 232 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OG1 THR R  64 "
            pdb=" OH  TYR R 144 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OD1 ASN A 292 "
            pdb=" OG1 THR A 364 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" O   LEU R  67 "
            pdb=" CD1 LEU R  71 "
     model   vdw
     2.319 3.460
  ... (remaining 59231 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:             1.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.370
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
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   0.056   7766  Z= 0.225
  Angle     :  0.797   8.527  10588  Z= 0.467
  Chirality :  0.052   0.226   1249
  Planarity :  0.006   0.064   1352
  Dihedral  : 14.282  98.876   2615
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  1.11 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.25), residues: 1021
  helix:  1.06 (0.26), residues: 379
  sheet: -0.12 (0.35), residues: 229
  loop : -1.79 (0.27), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 219 
 TYR   0.025   0.002   TYR N  60 
 PHE   0.017   0.002   PHE B 151 
 TRP   0.020   0.002   TRP B 339 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 7764)
  covalent geometry    : angle       0.79603 (10584)
  SS BOND              : bond        0.00448 (    2)
  SS BOND              : angle       1.73897 (    4)
  hydrogen bonds       : bond        0.15522 (  396)
  hydrogen bonds       : angle       5.83304 ( 1155)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 131
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A  320 THR cc_start: 0.8766 (t) cc_final: 0.8446 (m)
  outliers start: 2
  outliers final: 2
  residues processed: 132
  average time/residue: 0.0844
  time to fit residues: 14.6077
Evaluate side-chains
  110 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 108
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  281 VAL
Chi-restraints excluded: chain R residue  333 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.4980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
A  35 GLN
A 218 ASN
A 279 ASN
A 294 GLN
B 175 GLN
R 216 GLN
R 269 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.114887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.089162 restraints weight = 10861.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 2.05
r_work: 0.2807 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2687 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.1079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7766  Z= 0.160
  Angle     :  0.560   5.337  10588  Z= 0.301
  Chirality :  0.043   0.142   1249
  Planarity :  0.004   0.050   1352
  Dihedral  :  7.646  60.971   1150
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  6.93 %
    Favored  : 92.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.27), residues: 1021
  helix:  2.12 (0.27), residues: 389
  sheet: -0.23 (0.34), residues: 247
  loop : -1.58 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  72 
 TYR   0.011   0.001   TYR R 130 
 PHE   0.015   0.001   PHE B 151 
 TRP   0.013   0.002   TRP R 174 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 7764)
  covalent geometry    : angle       0.55976 (10584)
  SS BOND              : bond        0.00346 (    2)
  SS BOND              : angle       0.88853 (    4)
  hydrogen bonds       : bond        0.05236 (  396)
  hydrogen bonds       : angle       4.22973 ( 1155)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 0.304 
Fit side-chains
REVERT: B   78 LYS cc_start: 0.9059 (tppt) cc_final: 0.8849 (tptt)
REVERT: R  116 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8597 (tm-30)
REVERT: R  219 ARG cc_start: 0.7793 (ttp80) cc_final: 0.7576 (ttp80)
  outliers start: 7
  outliers final: 4
  residues processed: 119
  average time/residue: 0.1071
  time to fit residues: 16.4131
Evaluate side-chains
  111 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 107
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   40 VAL
Chi-restraints excluded: chain R residue  290 VAL
Chi-restraints excluded: chain R residue  331 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 96 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 92 optimal weight:    0.7980
   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  14 ASN
A  35 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.116360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.090489 restraints weight = 10694.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 2.06
r_work: 0.2841 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2721 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.1349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7766  Z= 0.125
  Angle     :  0.509   6.195  10588  Z= 0.272
  Chirality :  0.042   0.136   1249
  Planarity :  0.004   0.047   1352
  Dihedral  :  6.275  59.374   1145
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  9.02 %
    Favored  : 89.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.27), residues: 1021
  helix:  2.54 (0.27), residues: 388
  sheet: -0.08 (0.34), residues: 243
  loop : -1.51 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  72 
 TYR   0.010   0.001   TYR R 130 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.010   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7764)
  covalent geometry    : angle       0.50924 (10584)
  SS BOND              : bond        0.00332 (    2)
  SS BOND              : angle       0.58395 (    4)
  hydrogen bonds       : bond        0.04453 (  396)
  hydrogen bonds       : angle       3.91920 ( 1155)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 ASP cc_start: 0.8637 (m-30) cc_final: 0.8420 (m-30)
REVERT: A  378 ASP cc_start: 0.8850 (m-30) cc_final: 0.8649 (m-30)
REVERT: B   78 LYS cc_start: 0.9044 (tppt) cc_final: 0.8574 (tptt)
REVERT: N   93 VAL cc_start: 0.8841 (t) cc_final: 0.8627 (t)
REVERT: R   81 MET cc_start: 0.7980 (mmm) cc_final: 0.7741 (mtm)
  outliers start: 10
  outliers final: 7
  residues processed: 120
  average time/residue: 0.0932
  time to fit residues: 14.5017
Evaluate side-chains
  119 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   43 CYS
Chi-restraints excluded: chain R residue   72 VAL
Chi-restraints excluded: chain R residue   79 THR
Chi-restraints excluded: chain R residue  320 VAL
Chi-restraints excluded: chain R residue  331 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 14 optimal weight:    8.9990
   chunk 26 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0770
   chunk 24 optimal weight:    0.8980
   chunk 90 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
A  35 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.119606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.094129 restraints weight = 10801.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 2.02
r_work: 0.2856 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2738 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7766  Z= 0.115
  Angle     :  0.488   5.327  10588  Z= 0.262
  Chirality :  0.041   0.135   1249
  Planarity :  0.003   0.046   1352
  Dihedral  :  5.744  54.108   1145
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  9.85 %
    Favored  : 88.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.27), residues: 1021
  helix:  2.74 (0.27), residues: 388
  sheet:  0.03 (0.35), residues: 240
  loop : -1.42 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  72 
 TYR   0.012   0.001   TYR N  60 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.010   0.001   TRP R  85 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7764)
  covalent geometry    : angle       0.48791 (10584)
  SS BOND              : bond        0.00336 (    2)
  SS BOND              : angle       0.53688 (    4)
  hydrogen bonds       : bond        0.04211 (  396)
  hydrogen bonds       : angle       3.79099 ( 1155)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.190 
Fit side-chains
REVERT: B   78 LYS cc_start: 0.9056 (tppt) cc_final: 0.8609 (tptt)
REVERT: R  116 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8767 (tm-30)
REVERT: R  219 ARG cc_start: 0.7562 (ttp80) cc_final: 0.7319 (ttp80)
  outliers start: 10
  outliers final: 9
  residues processed: 120
  average time/residue: 0.1094
  time to fit residues: 16.9187
Evaluate side-chains
  119 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASN
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   72 VAL
Chi-restraints excluded: chain R residue  211 LEU
Chi-restraints excluded: chain R residue  320 VAL
Chi-restraints excluded: chain R residue  331 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
A  35 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.114027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.088274 restraints weight = 10828.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 2.06
r_work: 0.2811 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2692 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7766  Z= 0.153
  Angle     :  0.524   6.417  10588  Z= 0.282
  Chirality :  0.043   0.132   1249
  Planarity :  0.004   0.045   1352
  Dihedral  :  5.899  54.288   1145
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 10.54 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.27), residues: 1021
  helix:  2.76 (0.27), residues: 388
  sheet:  0.13 (0.35), residues: 235
  loop : -1.45 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  98 
 TYR   0.012   0.001   TYR N  60 
 PHE   0.017   0.001   PHE B 151 
 TRP   0.010   0.002   TRP R  85 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 7764)
  covalent geometry    : angle       0.52433 (10584)
  SS BOND              : bond        0.00442 (    2)
  SS BOND              : angle       0.71470 (    4)
  hydrogen bonds       : bond        0.04790 (  396)
  hydrogen bonds       : angle       3.88438 ( 1155)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.306 
Fit side-chains
REVERT: B   78 LYS cc_start: 0.9072 (tppt) cc_final: 0.8628 (tptt)
  outliers start: 12
  outliers final: 9
  residues processed: 119
  average time/residue: 0.0978
  time to fit residues: 14.9211
Evaluate side-chains
  117 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASN
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain R residue   72 VAL
Chi-restraints excluded: chain R residue  174 TRP
Chi-restraints excluded: chain R residue  320 VAL
Chi-restraints excluded: chain R residue  331 LEU
Chi-restraints excluded: chain R residue  332 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 63 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 76 optimal weight:    0.2980
   chunk 89 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
A  35 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.119944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.094721 restraints weight = 10698.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.2940 rms_B_bonded: 1.97
r_work: 0.2839 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2721 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7766  Z= 0.120
  Angle     :  0.485   5.401  10588  Z= 0.262
  Chirality :  0.042   0.134   1249
  Planarity :  0.003   0.045   1352
  Dihedral  :  5.683  58.840   1145
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.37 %
    Favored  : 86.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.27), residues: 1021
  helix:  2.86 (0.27), residues: 388
  sheet:  0.16 (0.35), residues: 232
  loop : -1.43 (0.29), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  98 
 TYR   0.011   0.001   TYR N  60 
 PHE   0.013   0.001   PHE B 151 
 TRP   0.010   0.001   TRP R  85 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 7764)
  covalent geometry    : angle       0.48520 (10584)
  SS BOND              : bond        0.00357 (    2)
  SS BOND              : angle       0.56377 (    4)
  hydrogen bonds       : bond        0.04304 (  396)
  hydrogen bonds       : angle       3.77299 ( 1155)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.266 
Fit side-chains
REVERT: B   78 LYS cc_start: 0.9074 (tppt) cc_final: 0.8640 (tptt)
REVERT: N   93 VAL cc_start: 0.8837 (t) cc_final: 0.8627 (t)
REVERT: R  291 ARG cc_start: 0.8639 (tpp-160) cc_final: 0.8360 (tpm170)
  outliers start: 12
  outliers final: 9
  residues processed: 118
  average time/residue: 0.0959
  time to fit residues: 14.7295
Evaluate side-chains
  116 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain R residue   72 VAL
Chi-restraints excluded: chain R residue  174 TRP
Chi-restraints excluded: chain R residue  320 VAL
Chi-restraints excluded: chain R residue  331 LEU
Chi-restraints excluded: chain R residue  332 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 15 optimal weight:    0.4980
   chunk 67 optimal weight:    0.0970
   chunk 69 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.117548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.091706 restraints weight = 10791.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 2.04
r_work: 0.2851 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2732 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7766  Z= 0.108
  Angle     :  0.474   6.623  10588  Z= 0.255
  Chirality :  0.041   0.135   1249
  Planarity :  0.003   0.045   1352
  Dihedral  :  5.100  43.285   1145
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 12.07 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.27), residues: 1021
  helix:  2.94 (0.27), residues: 388
  sheet:  0.37 (0.36), residues: 218
  loop : -1.43 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 219 
 TYR   0.014   0.001   TYR N  60 
 PHE   0.011   0.001   PHE B 151 
 TRP   0.011   0.001   TRP R  85 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 7764)
  covalent geometry    : angle       0.47358 (10584)
  SS BOND              : bond        0.00315 (    2)
  SS BOND              : angle       0.49499 (    4)
  hydrogen bonds       : bond        0.04027 (  396)
  hydrogen bonds       : angle       3.69951 ( 1155)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A  378 ASP cc_start: 0.8804 (m-30) cc_final: 0.8540 (m-30)
REVERT: B   78 LYS cc_start: 0.9059 (tppt) cc_final: 0.8629 (tptt)
REVERT: B  262 MET cc_start: 0.9118 (ttp) cc_final: 0.8863 (ttm)
REVERT: N   93 VAL cc_start: 0.8837 (t) cc_final: 0.8628 (t)
REVERT: R  116 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8673 (tm-30)
  outliers start: 12
  outliers final: 11
  residues processed: 121
  average time/residue: 0.0955
  time to fit residues: 14.9590
Evaluate side-chains
  120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain R residue   72 VAL
Chi-restraints excluded: chain R residue  174 TRP
Chi-restraints excluded: chain R residue  211 LEU
Chi-restraints excluded: chain R residue  311 ASP
Chi-restraints excluded: chain R residue  320 VAL
Chi-restraints excluded: chain R residue  331 LEU
Chi-restraints excluded: chain R residue  332 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   chunk 20 optimal weight:    0.2980
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 60 optimal weight:    0.3980
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.122439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.097361 restraints weight = 10615.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 1.96
r_work: 0.2858 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7766  Z= 0.108
  Angle     :  0.474   6.558  10588  Z= 0.254
  Chirality :  0.041   0.134   1249
  Planarity :  0.003   0.045   1352
  Dihedral  :  5.017  45.407   1145
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 11.65 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.27), residues: 1021
  helix:  2.94 (0.27), residues: 388
  sheet:  0.34 (0.36), residues: 220
  loop : -1.38 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 219 
 TYR   0.012   0.001   TYR N  60 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.011   0.001   TRP R  85 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 7764)
  covalent geometry    : angle       0.47350 (10584)
  SS BOND              : bond        0.00322 (    2)
  SS BOND              : angle       0.51264 (    4)
  hydrogen bonds       : bond        0.03994 (  396)
  hydrogen bonds       : angle       3.67677 ( 1155)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A  378 ASP cc_start: 0.8800 (m-30) cc_final: 0.8532 (m-30)
REVERT: B   78 LYS cc_start: 0.9064 (tppt) cc_final: 0.8638 (tptt)
REVERT: B  262 MET cc_start: 0.9092 (ttp) cc_final: 0.8847 (ttm)
REVERT: N   93 VAL cc_start: 0.8850 (t) cc_final: 0.8648 (t)
REVERT: R  116 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8698 (tm-30)
  outliers start: 16
  outliers final: 11
  residues processed: 123
  average time/residue: 0.1069
  time to fit residues: 17.1475
Evaluate side-chains
  116 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASN
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain R residue   21 VAL
Chi-restraints excluded: chain R residue  174 TRP
Chi-restraints excluded: chain R residue  311 ASP
Chi-restraints excluded: chain R residue  320 VAL
Chi-restraints excluded: chain R residue  331 LEU
Chi-restraints excluded: chain R residue  332 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 91 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   chunk 79 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.115940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.090010 restraints weight = 10876.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 2.07
r_work: 0.2828 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7766  Z= 0.129
  Angle     :  0.500   7.484  10588  Z= 0.269
  Chirality :  0.042   0.178   1249
  Planarity :  0.003   0.045   1352
  Dihedral  :  5.115  47.546   1145
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 11.79 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.27), residues: 1021
  helix:  2.90 (0.27), residues: 388
  sheet:  0.34 (0.36), residues: 220
  loop : -1.45 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 219 
 TYR   0.015   0.001   TYR N  60 
 PHE   0.014   0.001   PHE B 151 
 TRP   0.011   0.001   TRP R  85 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7764)
  covalent geometry    : angle       0.50027 (10584)
  SS BOND              : bond        0.00375 (    2)
  SS BOND              : angle       0.60733 (    4)
  hydrogen bonds       : bond        0.04301 (  396)
  hydrogen bonds       : angle       3.73717 ( 1155)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.202 
Fit side-chains
REVERT: B   78 LYS cc_start: 0.9061 (tppt) cc_final: 0.8637 (tptt)
REVERT: R  116 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8668 (tm-30)
  outliers start: 14
  outliers final: 11
  residues processed: 120
  average time/residue: 0.1162
  time to fit residues: 17.9964
Evaluate side-chains
  117 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASN
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain R residue  174 TRP
Chi-restraints excluded: chain R residue  211 LEU
Chi-restraints excluded: chain R residue  311 ASP
Chi-restraints excluded: chain R residue  320 VAL
Chi-restraints excluded: chain R residue  331 LEU
Chi-restraints excluded: chain R residue  332 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 87 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9980
   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  14 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.115945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.090026 restraints weight = 10771.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 2.07
r_work: 0.2833 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2714 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7766  Z= 0.128
  Angle     :  0.497   7.033  10588  Z= 0.267
  Chirality :  0.042   0.171   1249
  Planarity :  0.003   0.045   1352
  Dihedral  :  5.101  49.641   1145
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 12.21 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.27), residues: 1021
  helix:  2.91 (0.27), residues: 388
  sheet:  0.34 (0.36), residues: 215
  loop : -1.46 (0.28), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 219 
 TYR   0.014   0.001   TYR N  60 
 PHE   0.013   0.001   PHE B 151 
 TRP   0.012   0.001   TRP R  85 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7764)
  covalent geometry    : angle       0.49710 (10584)
  SS BOND              : bond        0.00363 (    2)
  SS BOND              : angle       0.63566 (    4)
  hydrogen bonds       : bond        0.04290 (  396)
  hydrogen bonds       : angle       3.74195 ( 1155)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A  378 ASP cc_start: 0.8724 (m-30) cc_final: 0.8484 (m-30)
REVERT: B   78 LYS cc_start: 0.9062 (tppt) cc_final: 0.8633 (tptt)
REVERT: G   52 THR cc_start: 0.7371 (OUTLIER) cc_final: 0.7116 (p)
REVERT: R  116 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8653 (tm-30)
  outliers start: 11
  outliers final: 10
  residues processed: 117
  average time/residue: 0.1016
  time to fit residues: 15.5525
Evaluate side-chains
  117 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ASN
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain R residue  174 TRP
Chi-restraints excluded: chain R residue  211 LEU
Chi-restraints excluded: chain R residue  311 ASP
Chi-restraints excluded: chain R residue  320 VAL
Chi-restraints excluded: chain R residue  331 LEU
Chi-restraints excluded: chain R residue  332 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 97 optimal weight:    0.4980
   chunk 31 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 78 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.121965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.096933 restraints weight = 10596.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.2951 rms_B_bonded: 1.96
r_work: 0.2851 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2732 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7766  Z= 0.116
  Angle     :  0.484   7.117  10588  Z= 0.260
  Chirality :  0.041   0.164   1249
  Planarity :  0.003   0.045   1352
  Dihedral  :  5.047  50.468   1145
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 12.34 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.27), residues: 1021
  helix:  2.93 (0.27), residues: 389
  sheet:  0.45 (0.36), residues: 212
  loop : -1.42 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 219 
 TYR   0.014   0.001   TYR N  60 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.012   0.001   TRP R  85 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 7764)
  covalent geometry    : angle       0.48400 (10584)
  SS BOND              : bond        0.00324 (    2)
  SS BOND              : angle       0.56406 (    4)
  hydrogen bonds       : bond        0.04076 (  396)
  hydrogen bonds       : angle       3.68826 ( 1155)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2076.26 seconds
wall clock time: 36 minutes 9.58 seconds (2169.58 seconds total)