Starting phenix.real_space_refine
on Fri Aug 22 17:26:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ge1_29952/08_2025/8ge1_29952.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ge1_29952/08_2025/8ge1_29952.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ge1_29952/08_2025/8ge1_29952.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ge1_29952/08_2025/8ge1_29952.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ge1_29952/08_2025/8ge1_29952.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ge1_29952/08_2025/8ge1_29952.cif"
  }
  resolution = 3.4
  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=  -0.001 sd=   0.035
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      39      5.16       5
     C    4169      2.51       5
     N    1133      2.21       5
     O    1123      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  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: 6464
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1670
          Classifications: {'peptide': 233}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 76}
          Link IDs: {'PTRANS': 6, 'TRANS': 226}
          Chain breaks: 3
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 273
          Unresolved non-hydrogen angles: 336
          Unresolved non-hydrogen dihedrals: 214
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'ARG:plan': 8, 'ASN:plan1': 4, 'GLU:plan': 16, 'GLN:plan1': 4, 'ASP:plan': 13, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 177
    Chain: "B"
      Number of atoms: 2349
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2349
          Classifications: {'peptide': 333}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 64}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
          Unresolved non-hydrogen bonds: 210
          Unresolved non-hydrogen angles: 263
          Unresolved non-hydrogen dihedrals: 157
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 4, 'GLU:plan': 6, 'ASN:plan1': 6, 'ASP:plan': 17}
          Unresolved non-hydrogen planarities: 149
    Chain: "G"
      Number of atoms: 356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 356
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 62
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "R"
      Number of atoms: 2074
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2074
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 75}
          Link IDs: {'PTRANS': 7, 'TRANS': 280}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 250
          Unresolved non-hydrogen angles: 313
          Unresolved non-hydrogen dihedrals: 200
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 9, 'TRP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 5, 'ARG:plan': 4, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 126
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.88, per 1000 atoms: 0.29
  Number of scatterers: 6464
  At special positions: 0
  Unit cell: (72.08, 97.52, 126.14, 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      39     16.00
     O    1123      8.00
     N    1133      7.00
     C    4169      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " 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: 0.59
  Conformation dependent library (CDL) restraints added in 504.5 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1720

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 8 sheets defined
      48.3% alpha, 17.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.806A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.544A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.612A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.538A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.371A  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 9 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.566A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 24
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'R' and resid 30 through 61
      removed outlier: 3.584A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 3.602A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.069A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.938A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 237
      removed outlier: 5.185A  pdb=" N   VAL R 210 " --> pdb=" O   VAL R 206 " (cutoff:3.500A)
      Proline residue:  R 211  - end of helix
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 4.531A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 3.871A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.483A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.998A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.041A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.420A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.188A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.147A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.016A  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: 3.611A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.651A  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: 6.252A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.997A  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: 3.547A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.374A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.912A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.648A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    1167 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.06

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2084
        1.34 -     1.45: 966
        1.45 -     1.57: 3501
        1.57 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 6605
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.450 -0.053 2.00e-02 2.50e+03 7.04e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.439 -0.045 2.00e-02 2.50e+03 5.11e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.567 -0.044 2.00e-02 2.50e+03 4.79e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 2.00e-02 2.50e+03 4.68e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" OAK G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.353  1.322  0.031 2.00e-02 2.50e+03 2.37e+00
  ... (remaining 6600 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 8882
        1.51 -     3.01: 118
        3.01 -     4.52: 21
        4.52 -     6.02: 12
        6.02 -     7.53: 2
  Bond angle restraints: 9035
  Sorted by residual:
  angle pdb=" N   GLN R 299 "
        pdb=" CA  GLN R 299 "
        pdb=" C   GLN R 299 "
      ideal   model   delta    sigma   weight residual
     113.56  108.25    5.31 1.39e+00 5.18e-01 1.46e+01
  angle pdb=" CA  GLN R 299 "
        pdb=" CB  GLN R 299 "
        pdb=" CG  GLN R 299 "
      ideal   model   delta    sigma   weight residual
     114.10  120.93   -6.83 2.00e+00 2.50e-01 1.17e+01
  angle pdb=" C   GLY A  49 "
        pdb=" N   GLU A  50 "
        pdb=" CA  GLU A  50 "
      ideal   model   delta    sigma   weight residual
     122.61  127.54   -4.93 1.56e+00 4.11e-01 9.97e+00
  angle pdb=" N   GLN R 231 "
        pdb=" CA  GLN R 231 "
        pdb=" CB  GLN R 231 "
      ideal   model   delta    sigma   weight residual
     110.28  115.07   -4.79 1.55e+00 4.16e-01 9.57e+00
  angle pdb=" C   ARG A 283 "
        pdb=" N   THR A 284 "
        pdb=" CA  THR A 284 "
      ideal   model   delta    sigma   weight residual
     123.47  127.84   -4.37 1.53e+00 4.27e-01 8.17e+00
  ... (remaining 9030 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 3525
       17.91 -    35.82: 248
       35.82 -    53.73: 33
       53.73 -    71.64: 4
       71.64 -    89.55: 2
  Dihedral angle restraints: 3812
    sinusoidal: 1164
      harmonic: 2648
  Sorted by residual:
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.49   16.51     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  LEU R 144 "
           pdb=" C   LEU R 144 "
           pdb=" N   LEU R 145 "
           pdb=" CA  LEU R 145 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.08   15.92     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CG  LYS B 209 "
           pdb=" CD  LYS B 209 "
           pdb=" CE  LYS B 209 "
           pdb=" NZ  LYS B 209 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  129.03   50.97     3      1.50e+01 4.44e-03 8.96e+00
  ... (remaining 3809 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 710
       0.033 -    0.065: 246
       0.065 -    0.098: 80
       0.098 -    0.130: 42
       0.130 -    0.163: 2
  Chirality restraints: 1080
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.56   -0.16 2.00e-01 2.50e+01 6.63e-01
  chirality pdb=" CA  GLN R 231 "
            pdb=" N   GLN R 231 "
            pdb=" C   GLN R 231 "
            pdb=" CB  GLN R 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.25e-01
  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    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  ... (remaining 1077 not shown)

  Planarity restraints: 1142
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 205 "   -0.008 2.00e-02 2.50e+03   1.56e-02 2.43e+00
        pdb=" C   ILE R 205 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ILE R 205 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   VAL R 206 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 343 "   -0.006 2.00e-02 2.50e+03   1.21e-02 1.46e+00
        pdb=" CG  ASP A 343 "    0.021 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 343 "   -0.007 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 343 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.010 2.00e-02 2.50e+03   7.96e-03 1.27e+00
        pdb=" CG  TYR B  59 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1139 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 585
        2.74 -     3.28: 6463
        3.28 -     3.82: 10904
        3.82 -     4.36: 11865
        4.36 -     4.90: 21836
  Nonbonded interactions: 51653
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 279 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   ARG A 283 "
            pdb=" OG1 THR A 284 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" O   HIS G  44 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" NH2 ARG R 221 "
            pdb=" OE2 GLU R 225 "
     model   vdw
     2.327 3.120
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.334 3.040
  ... (remaining 51648 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=0.00 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:             2.210
  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:             0.020
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.350
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6606  Z= 0.140
  Angle     :  0.506   7.531   9037  Z= 0.278
  Chirality :  0.041   0.163   1080
  Planarity :  0.003   0.027   1142
  Dihedral  : 12.486  89.546   2089
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  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:  1.67 (0.28), residues: 892
  helix:  2.56 (0.25), residues: 392
  sheet:  0.47 (0.38), residues: 168
  loop : -0.32 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 283 
 TYR   0.019   0.001   TYR B  59 
 PHE   0.016   0.001   PHE B 234 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6605)
  covalent geometry    : angle       0.50580 ( 9035)
  SS BOND              : bond        0.00238 (    1)
  SS BOND              : angle       0.30780 (    2)
  hydrogen bonds       : bond        0.17212 (  400)
  hydrogen bonds       : angle       6.23005 ( 1167)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A   60 MET cc_start: 0.8388 (mpp) cc_final: 0.8080 (mpp)
REVERT: A  343 ASP cc_start: 0.8477 (m-30) cc_final: 0.8208 (m-30)
REVERT: B   61 MET cc_start: 0.8325 (ppp) cc_final: 0.8110 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0765
  time to fit residues: 10.2474
Evaluate side-chains
  81 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
G  18 GLN
R  93 HIS
** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.122001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.108000 restraints weight = 10301.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 1.81
r_work: 0.3252 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.0970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6606  Z= 0.130
  Angle     :  0.490   7.444   9037  Z= 0.265
  Chirality :  0.042   0.142   1080
  Planarity :  0.003   0.023   1142
  Dihedral  :  3.969  23.894    980
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  7.62 %
    Favored  : 91.47 %
  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:  1.88 (0.28), residues: 892
  helix:  2.74 (0.25), residues: 402
  sheet:  0.55 (0.38), residues: 162
  loop : -0.28 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 283 
 TYR   0.018   0.001   TYR B  59 
 PHE   0.010   0.001   PHE R 240 
 TRP   0.025   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R  93 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6605)
  covalent geometry    : angle       0.48972 ( 9035)
  SS BOND              : bond        0.00101 (    1)
  SS BOND              : angle       0.22341 (    2)
  hydrogen bonds       : bond        0.04290 (  400)
  hydrogen bonds       : angle       4.57073 ( 1167)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.253 
Fit side-chains
REVERT: R   93 HIS cc_start: 0.8739 (OUTLIER) cc_final: 0.8525 (t-90)
  outliers start: 5
  outliers final: 3
  residues processed: 95
  average time/residue: 0.0798
  time to fit residues: 10.4067
Evaluate side-chains
  86 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain R residue   93 HIS
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  228 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 31 optimal weight:    7.9990
   chunk 17 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 56 optimal weight:    9.9990
   chunk 35 optimal weight:    9.9990
   chunk 38 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
R  93 HIS
** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.116287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.102088 restraints weight = 10570.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 1.86
r_work: 0.3181 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   6606  Z= 0.246
  Angle     :  0.546   7.846   9037  Z= 0.297
  Chirality :  0.044   0.135   1080
  Planarity :  0.003   0.023   1142
  Dihedral  :  4.263  25.452    980
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 11.98 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.73 (0.28), residues: 892
  helix:  2.60 (0.25), residues: 396
  sheet:  0.52 (0.38), residues: 168
  loop : -0.31 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 283 
 TYR   0.025   0.002   TYR B  59 
 PHE   0.015   0.002   PHE R 289 
 TRP   0.023   0.002   TRP B  82 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00575 ( 6605)
  covalent geometry    : angle       0.54619 ( 9035)
  SS BOND              : bond        0.00179 (    1)
  SS BOND              : angle       0.14322 (    2)
  hydrogen bonds       : bond        0.04703 (  400)
  hydrogen bonds       : angle       4.45558 ( 1167)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  343 ASP cc_start: 0.8725 (m-30) cc_final: 0.8409 (m-30)
REVERT: R   93 HIS cc_start: 0.8925 (OUTLIER) cc_final: 0.8720 (t-90)
  outliers start: 13
  outliers final: 4
  residues processed: 89
  average time/residue: 0.0683
  time to fit residues: 8.7114
Evaluate side-chains
  79 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   93 HIS
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  228 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 66 optimal weight:    0.2980
   chunk 88 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 36 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 294 GLN
R  93 HIS
** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.119832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.105595 restraints weight = 10500.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.86
r_work: 0.3230 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6606  Z= 0.125
  Angle     :  0.468   7.224   9037  Z= 0.251
  Chirality :  0.042   0.146   1080
  Planarity :  0.003   0.025   1142
  Dihedral  :  4.020  24.967    980
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 13.25 %
    Favored  : 84.21 %
  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:  1.83 (0.28), residues: 892
  helix:  2.76 (0.25), residues: 396
  sheet:  0.52 (0.38), residues: 164
  loop : -0.34 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.015   0.001   TYR B  59 
 PHE   0.009   0.001   PHE R 282 
 TRP   0.022   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6605)
  covalent geometry    : angle       0.46763 ( 9035)
  SS BOND              : bond        0.00070 (    1)
  SS BOND              : angle       0.17376 (    2)
  hydrogen bonds       : bond        0.03945 (  400)
  hydrogen bonds       : angle       4.15233 ( 1167)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 ASP cc_start: 0.8693 (m-30) cc_final: 0.8266 (m-30)
REVERT: R   51 ASN cc_start: 0.7903 (m-40) cc_final: 0.7235 (m110)
REVERT: R   93 HIS cc_start: 0.8905 (OUTLIER) cc_final: 0.8696 (t-90)
  outliers start: 14
  outliers final: 8
  residues processed: 96
  average time/residue: 0.0861
  time to fit residues: 11.4394
Evaluate side-chains
  86 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   93 HIS
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  228 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0870
   chunk 67 optimal weight:    0.9980
   chunk 76 optimal weight:    0.4980
   chunk 46 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0060
   chunk 29 optimal weight:    3.9990
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.3974

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

Flipped N/Q/H residues before XYZ refinement:
R  93 HIS
** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.121145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.106841 restraints weight = 10522.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 1.89
r_work: 0.3262 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6606  Z= 0.099
  Angle     :  0.451   6.873   9037  Z= 0.238
  Chirality :  0.041   0.143   1080
  Planarity :  0.003   0.023   1142
  Dihedral  :  3.853  24.201    980
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 13.79 %
    Favored  : 83.48 %
  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:  2.00 (0.28), residues: 892
  helix:  2.97 (0.25), residues: 396
  sheet:  0.61 (0.38), residues: 163
  loop : -0.35 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 283 
 TYR   0.016   0.001   TYR A 253 
 PHE   0.008   0.001   PHE R 282 
 TRP   0.021   0.001   TRP B  82 
 HIS   0.004   0.000   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 6605)
  covalent geometry    : angle       0.45092 ( 9035)
  SS BOND              : bond        0.00069 (    1)
  SS BOND              : angle       0.20794 (    2)
  hydrogen bonds       : bond        0.03604 (  400)
  hydrogen bonds       : angle       3.98326 ( 1167)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A  233 LYS cc_start: 0.8830 (tppt) cc_final: 0.8545 (mmmm)
REVERT: A  343 ASP cc_start: 0.8675 (m-30) cc_final: 0.8105 (m-30)
REVERT: B   59 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.8194 (m-80)
REVERT: R   51 ASN cc_start: 0.7814 (m-40) cc_final: 0.7431 (m110)
REVERT: R   93 HIS cc_start: 0.8770 (OUTLIER) cc_final: 0.8557 (t-90)
REVERT: R  318 ASN cc_start: 0.8774 (t0) cc_final: 0.8180 (t0)
  outliers start: 15
  outliers final: 7
  residues processed: 94
  average time/residue: 0.0844
  time to fit residues: 10.7580
Evaluate side-chains
  89 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   93 HIS
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  228 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0670
   chunk 34 optimal weight:    3.9990
   chunk 83 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 10 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
R  93 HIS
** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.120957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.106573 restraints weight = 10489.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 1.90
r_work: 0.3258 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6606  Z= 0.111
  Angle     :  0.449   6.600   9037  Z= 0.238
  Chirality :  0.041   0.143   1080
  Planarity :  0.003   0.024   1142
  Dihedral  :  3.797  23.530    980
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 14.88 %
    Favored  : 82.21 %
  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:  2.01 (0.28), residues: 892
  helix:  3.01 (0.25), residues: 396
  sheet:  0.57 (0.38), residues: 163
  loop : -0.36 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 283 
 TYR   0.017   0.001   TYR A 253 
 PHE   0.009   0.001   PHE R 282 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.004   0.000   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 6605)
  covalent geometry    : angle       0.44952 ( 9035)
  SS BOND              : bond        0.00087 (    1)
  SS BOND              : angle       0.21792 (    2)
  hydrogen bonds       : bond        0.03582 (  400)
  hydrogen bonds       : angle       3.91714 ( 1167)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A  233 LYS cc_start: 0.8831 (tppt) cc_final: 0.8514 (mmmm)
REVERT: A  343 ASP cc_start: 0.8670 (m-30) cc_final: 0.8147 (m-30)
REVERT: B   59 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.8220 (m-80)
REVERT: R   51 ASN cc_start: 0.7791 (m-40) cc_final: 0.7376 (m110)
REVERT: R  231 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8196 (tm-30)
REVERT: R  318 ASN cc_start: 0.8734 (t0) cc_final: 0.8138 (t0)
  outliers start: 16
  outliers final: 10
  residues processed: 95
  average time/residue: 0.0850
  time to fit residues: 10.9621
Evaluate side-chains
  92 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  228 ARG
Chi-restraints excluded: chain R residue  231 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 76 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.119865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.105390 restraints weight = 10522.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.90
r_work: 0.3215 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6606  Z= 0.134
  Angle     :  0.465   6.426   9037  Z= 0.246
  Chirality :  0.041   0.142   1080
  Planarity :  0.003   0.024   1142
  Dihedral  :  3.846  22.951    980
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 15.79 %
    Favored  : 80.76 %
  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:  1.99 (0.29), residues: 892
  helix:  3.03 (0.25), residues: 396
  sheet:  0.35 (0.37), residues: 171
  loop : -0.30 (0.35), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 283 
 TYR   0.017   0.001   TYR A 253 
 PHE   0.011   0.001   PHE R 289 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.002   0.000   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6605)
  covalent geometry    : angle       0.46533 ( 9035)
  SS BOND              : bond        0.00084 (    1)
  SS BOND              : angle       0.18754 (    2)
  hydrogen bonds       : bond        0.03737 (  400)
  hydrogen bonds       : angle       3.91288 ( 1167)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  343 ASP cc_start: 0.8686 (m-30) cc_final: 0.8210 (m-30)
REVERT: B   59 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.8230 (m-80)
REVERT: R  231 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8176 (tm-30)
REVERT: R  318 ASN cc_start: 0.8774 (t0) cc_final: 0.8168 (t0)
  outliers start: 19
  outliers final: 13
  residues processed: 93
  average time/residue: 0.0752
  time to fit residues: 9.8681
Evaluate side-chains
  91 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   82 MET
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  228 ARG
Chi-restraints excluded: chain R residue  231 GLN
Chi-restraints excluded: chain R residue  292 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 61 optimal weight:   20.0000
   chunk 36 optimal weight:    0.0670
   chunk 42 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 22 optimal weight:    0.3980
   chunk 3 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 56 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.120930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.106462 restraints weight = 10477.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.90
r_work: 0.3229 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6606  Z= 0.112
  Angle     :  0.465   6.376   9037  Z= 0.245
  Chirality :  0.041   0.144   1080
  Planarity :  0.003   0.023   1142
  Dihedral  :  3.775  22.781    980
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 16.15 %
    Favored  : 80.22 %
  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:  2.03 (0.29), residues: 892
  helix:  3.07 (0.25), residues: 396
  sheet:  0.37 (0.37), residues: 171
  loop : -0.31 (0.35), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 283 
 TYR   0.018   0.001   TYR A 253 
 PHE   0.009   0.001   PHE R 289 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.004   0.000   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 6605)
  covalent geometry    : angle       0.46509 ( 9035)
  SS BOND              : bond        0.00060 (    1)
  SS BOND              : angle       0.19573 (    2)
  hydrogen bonds       : bond        0.03562 (  400)
  hydrogen bonds       : angle       3.87573 ( 1167)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  213 GLN cc_start: 0.8672 (pp30) cc_final: 0.8227 (tt0)
REVERT: A  343 ASP cc_start: 0.8696 (m-30) cc_final: 0.8259 (m-30)
REVERT: B   59 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.8217 (m-80)
REVERT: R   51 ASN cc_start: 0.7814 (m-40) cc_final: 0.7457 (m110)
REVERT: R  231 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8154 (tm-30)
REVERT: R  318 ASN cc_start: 0.8763 (t0) cc_final: 0.8157 (t0)
  outliers start: 20
  outliers final: 13
  residues processed: 95
  average time/residue: 0.0775
  time to fit residues: 10.2040
Evaluate side-chains
  93 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  228 ARG
Chi-restraints excluded: chain R residue  231 GLN
Chi-restraints excluded: chain R residue  292 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 80 optimal weight:    0.4980
   chunk 38 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   chunk 86 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   chunk 70 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.109161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.091057 restraints weight = 11372.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 2.69
r_work: 0.3013 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6606  Z= 0.115
  Angle     :  0.465   6.917   9037  Z= 0.244
  Chirality :  0.041   0.145   1080
  Planarity :  0.003   0.024   1142
  Dihedral  :  3.769  22.516    980
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 16.15 %
    Favored  : 80.40 %
  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:  2.00 (0.29), residues: 892
  helix:  3.03 (0.25), residues: 396
  sheet:  0.42 (0.37), residues: 170
  loop : -0.32 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 231 
 TYR   0.019   0.001   TYR A 253 
 PHE   0.009   0.001   PHE B 234 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6605)
  covalent geometry    : angle       0.46524 ( 9035)
  SS BOND              : bond        0.00058 (    1)
  SS BOND              : angle       0.23052 (    2)
  hydrogen bonds       : bond        0.03591 (  400)
  hydrogen bonds       : angle       3.86835 ( 1167)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A   60 MET cc_start: 0.8522 (mpp) cc_final: 0.8280 (mpp)
REVERT: A  213 GLN cc_start: 0.8635 (pp30) cc_final: 0.8245 (tt0)
REVERT: A  233 LYS cc_start: 0.8592 (tttt) cc_final: 0.8321 (ttmm)
REVERT: A  343 ASP cc_start: 0.8777 (m-30) cc_final: 0.8260 (m-30)
REVERT: B   59 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7788 (m-80)
REVERT: G   48 ASP cc_start: 0.8479 (t0) cc_final: 0.8275 (t0)
REVERT: R   51 ASN cc_start: 0.7584 (m-40) cc_final: 0.7216 (m110)
REVERT: R  231 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7726 (tm-30)
REVERT: R  318 ASN cc_start: 0.8777 (t0) cc_final: 0.7998 (t0)
  outliers start: 19
  outliers final: 13
  residues processed: 96
  average time/residue: 0.0826
  time to fit residues: 10.8569
Evaluate side-chains
  93 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  228 ARG
Chi-restraints excluded: chain R residue  231 GLN
Chi-restraints excluded: chain R residue  292 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 72 optimal weight:    0.0370
   chunk 45 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 85 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.7258

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

Flipped N/Q/H residues before XYZ refinement:
** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.120917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.106446 restraints weight = 10362.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 1.90
r_work: 0.3232 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6606  Z= 0.118
  Angle     :  0.463   6.904   9037  Z= 0.243
  Chirality :  0.041   0.145   1080
  Planarity :  0.003   0.024   1142
  Dihedral  :  3.762  22.463    980
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 16.33 %
    Favored  : 80.58 %
  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:  2.00 (0.28), residues: 892
  helix:  3.00 (0.25), residues: 396
  sheet:  0.57 (0.38), residues: 164
  loop : -0.37 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 283 
 TYR   0.020   0.001   TYR A 253 
 PHE   0.009   0.001   PHE R 289 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.005   0.000   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6605)
  covalent geometry    : angle       0.46271 ( 9035)
  SS BOND              : bond        0.00065 (    1)
  SS BOND              : angle       0.25065 (    2)
  hydrogen bonds       : bond        0.03581 (  400)
  hydrogen bonds       : angle       3.85694 ( 1167)

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

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

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1784 Ramachandran restraints generated.
    892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  213 GLN cc_start: 0.8660 (pp30) cc_final: 0.8243 (tt0)
REVERT: A  343 ASP cc_start: 0.8665 (m-30) cc_final: 0.8221 (m-30)
REVERT: B   59 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.8228 (m-80)
REVERT: R  231 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8161 (tm-30)
REVERT: R  318 ASN cc_start: 0.8743 (t0) cc_final: 0.8186 (t0)
  outliers start: 17
  outliers final: 14
  residues processed: 95
  average time/residue: 0.0816
  time to fit residues: 10.5523
Evaluate side-chains
  92 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  228 ARG
Chi-restraints excluded: chain R residue  231 GLN
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 61 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 72 optimal weight:    0.0170
   chunk 55 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 76 optimal weight:    0.0870
   chunk 79 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 37 optimal weight:    0.3980
   overall best weight:    0.3996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.110550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.092617 restraints weight = 11238.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 2.69
r_work: 0.3041 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   6606  Z= 0.098
  Angle     :  0.451   7.026   9037  Z= 0.239
  Chirality :  0.041   0.166   1080
  Planarity :  0.003   0.024   1142
  Dihedral  :  3.680  22.501    980
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 17.24 %
    Favored  : 79.85 %
  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:  2.08 (0.29), residues: 892
  helix:  3.03 (0.25), residues: 396
  sheet:  0.84 (0.39), residues: 157
  loop : -0.40 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 283 
 TYR   0.019   0.001   TYR A 253 
 PHE   0.008   0.001   PHE B 234 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 6605)
  covalent geometry    : angle       0.45073 ( 9035)
  SS BOND              : bond        0.00049 (    1)
  SS BOND              : angle       0.31032 (    2)
  hydrogen bonds       : bond        0.03424 (  400)
  hydrogen bonds       : angle       3.84445 ( 1167)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1604.23 seconds
wall clock time: 28 minutes 18.04 seconds (1698.04 seconds total)