Starting phenix.real_space_refine
on Tue Mar 11 18:30:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ge9_29961/03_2025/8ge9_29961.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ge9_29961/03_2025/8ge9_29961.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ge9_29961/03_2025/8ge9_29961.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ge9_29961/03_2025/8ge9_29961.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ge9_29961/03_2025/8ge9_29961.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ge9_29961/03_2025/8ge9_29961.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.031
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      44      5.16       5
     C    4201      2.51       5
     N    1121      2.21       5
     O    1153      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6519
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1705
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 65}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 254
          Unresolved non-hydrogen angles: 305
          Unresolved non-hydrogen dihedrals: 207
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 1, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 10}
          Unresolved non-hydrogen planarities: 174
    Chain: "B"
      Number of atoms: 2393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2393
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 5, 'TRANS': 325}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 151
          Unresolved non-hydrogen angles: 186
          Unresolved non-hydrogen dihedrals: 116
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 11}
          Unresolved non-hydrogen planarities: 123
    Chain: "G"
      Number of atoms: 335
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 335
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 58
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 39
    Chain: "R"
      Number of atoms: 2070
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2070
          Classifications: {'peptide': 282}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'PTRANS': 7, 'TRANS': 274}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 201
          Unresolved non-hydrogen angles: 247
          Unresolved non-hydrogen dihedrals: 164
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 8, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 109
    Chain: "R"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 4.30, per 1000 atoms: 0.66
  Number of scatterers: 6519
  At special positions: 0
  Unit cell: (68.9, 96.46, 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      44     16.00
     O    1153      8.00
     N    1121      7.00
     C    4201      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: 1.45
  Conformation dependent library (CDL) restraints added in 991.9 milliseconds
  

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1704

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 8 sheets defined
      48.1% alpha, 16.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 40
      removed outlier: 3.569A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   THR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
      removed outlier: 3.610A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 237
    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: 3.667A  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: 3.785A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 7 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.702A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 12 through 24
      removed outlier: 3.915A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 31 through 61
      removed outlier: 3.611A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 3.757A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.245A  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
      removed outlier: 3.560A  pdb=" N   SER R 137 " --> pdb=" O   PHE R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.420A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 5.055A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.867A  pdb=" N   ILE R 201 " --> pdb=" O   GLN R 197 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 236
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.903A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.940A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 3.875A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 3.905A  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: 4.661A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.800A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.417A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.146A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.406A  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: 6.727A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.453A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL B  71 " --> pdb=" O   HIS B  62 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 6.428A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.508A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.812A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.286A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234
      removed outlier: 3.531A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.933A  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: 6.160A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    391 hydrogen bonds defined for protein.
    1137 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.13

  Time building geometry restraints manager: 1.75 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: 2101
        1.34 -     1.46: 1560
        1.46 -     1.58: 2937
        1.58 -     1.70: 1
        1.70 -     1.81: 60
  Bond restraints: 6659
  Sorted by residual:
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.594 -0.071 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.451 -0.054 2.00e-02 2.50e+03 7.22e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.440 -0.046 2.00e-02 2.50e+03 5.33e+00
  bond pdb=" CAF G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.519  1.558 -0.039 2.00e-02 2.50e+03 3.81e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 2.00e-02 2.50e+03 3.69e+00
  ... (remaining 6654 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 8756
        1.25 -     2.49: 274
        2.49 -     3.74: 63
        3.74 -     4.99: 12
        4.99 -     6.24: 6
  Bond angle restraints: 9111
  Sorted by residual:
  angle pdb=" N   ILE A 257 "
        pdb=" CA  ILE A 257 "
        pdb=" C   ILE A 257 "
      ideal   model   delta    sigma   weight residual
     106.21  110.10   -3.89 1.07e+00 8.73e-01 1.32e+01
  angle pdb=" C   GLY A 226 "
        pdb=" N   GLN A 227 "
        pdb=" CA  GLN A 227 "
      ideal   model   delta    sigma   weight residual
     121.54  127.50   -5.96 1.91e+00 2.74e-01 9.75e+00
  angle pdb=" C   TYR B  59 "
        pdb=" N   ALA B  60 "
        pdb=" CA  ALA B  60 "
      ideal   model   delta    sigma   weight residual
     122.37  118.41    3.96 1.72e+00 3.38e-01 5.29e+00
  angle pdb=" CA  GLY B  53 "
        pdb=" C   GLY B  53 "
        pdb=" N   HIS B  54 "
      ideal   model   delta    sigma   weight residual
     116.69  121.22   -4.53 2.04e+00 2.40e-01 4.94e+00
  angle pdb=" CAG G1I R 501 "
        pdb=" CAH G1I R 501 "
        pdb=" CAI G1I R 501 "
      ideal   model   delta    sigma   weight residual
     110.89  117.13   -6.24 3.00e+00 1.11e-01 4.32e+00
  ... (remaining 9106 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 3565
       17.97 -    35.94: 229
       35.94 -    53.91: 39
       53.91 -    71.87: 6
       71.87 -    89.84: 5
  Dihedral angle restraints: 3844
    sinusoidal: 1220
      harmonic: 2624
  Sorted by residual:
  dihedral pdb=" CA  PHE R 208 "
           pdb=" C   PHE R 208 "
           pdb=" N   TYR R 209 "
           pdb=" CA  TYR R 209 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.33  -18.67     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  PRO B 194 "
           pdb=" C   PRO B 194 "
           pdb=" N   ASP B 195 "
           pdb=" CA  ASP B 195 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.76   16.24     0      5.00e+00 4.00e-02 1.05e+01
  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  163.83   16.17     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 3841 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 737
       0.031 -    0.062: 235
       0.062 -    0.093: 85
       0.093 -    0.124: 37
       0.124 -    0.155: 5
  Chirality restraints: 1099
  Sorted by residual:
  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    2.59   -0.15 2.00e-01 2.50e+01 5.97e-01
  chirality pdb=" CB  ILE A  56 "
            pdb=" CA  ILE A  56 "
            pdb=" CG1 ILE A  56 "
            pdb=" CG2 ILE A  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.79   -0.14 2.00e-01 2.50e+01 5.17e-01
  chirality pdb=" CA  ILE B 338 "
            pdb=" N   ILE B 338 "
            pdb=" C   ILE B 338 "
            pdb=" CB  ILE B 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.10e-01
  ... (remaining 1096 not shown)

  Planarity restraints: 1145
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 205 "   -0.007 2.00e-02 2.50e+03   1.38e-02 1.90e+00
        pdb=" C   ILE R 205 "    0.024 2.00e-02 2.50e+03
        pdb=" O   ILE R 205 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   VAL R 206 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL G  54 "   -0.022 5.00e-02 4.00e+02   3.38e-02 1.82e+00
        pdb=" N   PRO G  55 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO G  55 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO G  55 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R  49 "   -0.007 2.00e-02 2.50e+03   9.93e-03 1.73e+00
        pdb=" CG  PHE R  49 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 PHE R  49 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE R  49 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE R  49 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE R  49 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE R  49 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1142 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 803
        2.75 -     3.29: 6519
        3.29 -     3.83: 11221
        3.83 -     4.36: 12317
        4.36 -     4.90: 22357
  Nonbonded interactions: 53217
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OG  SER R 319 "
            pdb=" O   HOH R 601 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OH  TYR B 145 "
            pdb=" OD2 ASP B 186 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" NH1 ARG B 314 "
     model   vdw
     2.285 3.120
  ... (remaining 53212 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 group one per residue
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:             1.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.080
  Find NCS groups from input model:        0.080
  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:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
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   0.071   6659  Z= 0.209
  Angle     :  0.561   6.237   9111  Z= 0.317
  Chirality :  0.038   0.155   1099
  Planarity :  0.003   0.034   1145
  Dihedral  : 13.036  89.842   2137
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.28), residues: 884
  helix:  2.34 (0.26), residues: 396
  sheet:  0.88 (0.41), residues: 168
  loop : -0.93 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 105 
 HIS   0.010   0.001   HIS B  54 
 PHE   0.023   0.001   PHE R  49 
 TYR   0.010   0.001   TYR R 199 
 ARG   0.002   0.000   ARG B 283 

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.8277 (mtmt) cc_final: 0.8063 (mtpt)
REVERT: B  243 THR cc_start: 0.8640 (p) cc_final: 0.8426 (p)
REVERT: R   52 VAL cc_start: 0.9043 (t) cc_final: 0.8775 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1613
  time to fit residues: 24.9206
Evaluate side-chains
  87 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 23 optimal weight:    9.9990
   chunk 45 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 69 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.133307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.113887 restraints weight = 10271.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.117136 restraints weight = 6107.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.119292 restraints weight = 4286.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.1014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6659  Z= 0.219
  Angle     :  0.507   7.809   9111  Z= 0.279
  Chirality :  0.041   0.159   1099
  Planarity :  0.003   0.034   1145
  Dihedral  :  4.898  62.416    968
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  8.38 %
    Favored  : 90.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.28), residues: 884
  helix:  2.71 (0.26), residues: 382
  sheet:  0.49 (0.39), residues: 179
  loop : -0.91 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 339 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.017   0.002   PHE R  49 
 TYR   0.021   0.002   TYR A 318 
 ARG   0.003   0.000   ARG B 314 

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8232 (tp40) cc_final: 0.7963 (tp-100)
REVERT: A  309 GLU cc_start: 0.7795 (pm20) cc_final: 0.7557 (mp0)
REVERT: B  147 SER cc_start: 0.8847 (m) cc_final: 0.8484 (t)
  outliers start: 7
  outliers final: 5
  residues processed: 98
  average time/residue: 0.1610
  time to fit residues: 22.3787
Evaluate side-chains
  89 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain R residue   39 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.131546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.112233 restraints weight = 10291.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.115433 restraints weight = 6121.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.117658 restraints weight = 4309.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6659  Z= 0.222
  Angle     :  0.493   5.723   9111  Z= 0.271
  Chirality :  0.040   0.162   1099
  Planarity :  0.003   0.034   1145
  Dihedral  :  4.782  57.941    968
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 12.40 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.28), residues: 884
  helix:  2.78 (0.26), residues: 382
  sheet:  0.31 (0.38), residues: 181
  loop : -0.89 (0.32), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.014   0.001   PHE B 241 
 TYR   0.015   0.001   TYR R 199 
 ARG   0.002   0.000   ARG B 314 

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8319 (tp40) cc_final: 0.8038 (tp-100)
REVERT: A  309 GLU cc_start: 0.7759 (pm20) cc_final: 0.7490 (mp0)
REVERT: B  147 SER cc_start: 0.8793 (m) cc_final: 0.8430 (t)
  outliers start: 7
  outliers final: 5
  residues processed: 92
  average time/residue: 0.1581
  time to fit residues: 20.6641
Evaluate side-chains
  85 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue   39 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 61 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 72 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.132005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.112452 restraints weight = 10487.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.115746 restraints weight = 6222.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.118010 restraints weight = 4354.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6659  Z= 0.197
  Angle     :  0.471   5.636   9111  Z= 0.259
  Chirality :  0.040   0.154   1099
  Planarity :  0.003   0.033   1145
  Dihedral  :  4.642  52.681    968
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 14.07 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.29), residues: 884
  helix:  2.79 (0.26), residues: 386
  sheet:  0.18 (0.38), residues: 186
  loop : -0.89 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.019   0.001   PHE R  49 
 TYR   0.024   0.001   TYR A 318 
 ARG   0.002   0.000   ARG B 137 

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8303 (tp40) cc_final: 0.8017 (tp-100)
REVERT: A  309 GLU cc_start: 0.7773 (pm20) cc_final: 0.7514 (mp0)
REVERT: B  147 SER cc_start: 0.8772 (m) cc_final: 0.8517 (t)
REVERT: R   86 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8688 (m)
REVERT: R  173 TRP cc_start: 0.7595 (m-10) cc_final: 0.6428 (m100)
  outliers start: 12
  outliers final: 8
  residues processed: 89
  average time/residue: 0.1416
  time to fit residues: 18.7796
Evaluate side-chains
  86 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue   39 VAL
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0980
   chunk 12 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.129337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.110796 restraints weight = 10078.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.113975 restraints weight = 5974.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.116132 restraints weight = 4171.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
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      :  0.003   0.036   6659  Z= 0.196
  Angle     :  0.469   5.562   9111  Z= 0.259
  Chirality :  0.039   0.150   1099
  Planarity :  0.003   0.033   1145
  Dihedral  :  4.526  46.946    968
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 14.57 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.29), residues: 884
  helix:  2.74 (0.26), residues: 385
  sheet:  0.12 (0.38), residues: 184
  loop : -0.85 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.012   0.001   PHE R 289 
 TYR   0.014   0.001   TYR R 199 
 ARG   0.002   0.000   ARG B 137 

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8299 (tp40) cc_final: 0.8014 (tp-100)
REVERT: A  309 GLU cc_start: 0.7764 (pm20) cc_final: 0.7520 (mp0)
REVERT: B  338 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8331 (mt)
REVERT: R   86 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8588 (m)
REVERT: R  173 TRP cc_start: 0.7464 (m-10) cc_final: 0.6463 (m100)
  outliers start: 12
  outliers final: 7
  residues processed: 94
  average time/residue: 0.1328
  time to fit residues: 18.7252
Evaluate side-chains
  88 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue   39 VAL
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 15 optimal weight:    0.2980
   chunk 72 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 88 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0970
   chunk 66 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.132496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.113109 restraints weight = 10269.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.116414 restraints weight = 6112.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.118626 restraints weight = 4263.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6659  Z= 0.169
  Angle     :  0.461   5.615   9111  Z= 0.251
  Chirality :  0.039   0.153   1099
  Planarity :  0.003   0.033   1145
  Dihedral  :  4.389  39.907    968
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 17.25 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.28), residues: 884
  helix:  2.80 (0.26), residues: 385
  sheet:  0.08 (0.38), residues: 184
  loop : -0.85 (0.32), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.022   0.001   PHE R  49 
 TYR   0.013   0.001   TYR R 199 
 ARG   0.002   0.000   ARG B 137 

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8301 (tp40) cc_final: 0.7985 (tp-100)
REVERT: A  309 GLU cc_start: 0.7771 (pm20) cc_final: 0.7516 (mp0)
REVERT: B  338 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8285 (mt)
REVERT: R   86 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8576 (m)
  outliers start: 11
  outliers final: 8
  residues processed: 93
  average time/residue: 0.1488
  time to fit residues: 20.0034
Evaluate side-chains
  91 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain R residue   39 VAL
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 57 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0570
   chunk 15 optimal weight:    0.2980
   chunk 13 optimal weight:    0.9980
   chunk 77 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.132001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.112746 restraints weight = 10284.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.116037 restraints weight = 6109.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.118236 restraints weight = 4258.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6659  Z= 0.178
  Angle     :  0.458   5.601   9111  Z= 0.250
  Chirality :  0.039   0.154   1099
  Planarity :  0.003   0.033   1145
  Dihedral  :  4.306  35.064    968
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.59 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.28), residues: 884
  helix:  2.86 (0.26), residues: 386
  sheet:  0.04 (0.38), residues: 184
  loop : -0.90 (0.32), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP R 173 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.012   0.001   PHE R 289 
 TYR   0.014   0.001   TYR R 199 
 ARG   0.002   0.000   ARG B 137 

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8303 (tp40) cc_final: 0.7999 (tp-100)
REVERT: A  309 GLU cc_start: 0.7726 (pm20) cc_final: 0.7479 (mp0)
REVERT: B  338 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8299 (mt)
REVERT: R   86 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8571 (m)
  outliers start: 14
  outliers final: 10
  residues processed: 96
  average time/residue: 0.1509
  time to fit residues: 21.1244
Evaluate side-chains
  93 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain R residue   39 VAL
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  317 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0870
   chunk 84 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 29 optimal weight:    0.4980
   chunk 18 optimal weight:    1.9990
   chunk 86 optimal weight:    0.5980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.132023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.112746 restraints weight = 10308.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.116025 restraints weight = 6089.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.118239 restraints weight = 4241.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6659  Z= 0.178
  Angle     :  0.455   5.590   9111  Z= 0.249
  Chirality :  0.039   0.152   1099
  Planarity :  0.003   0.034   1145
  Dihedral  :  4.280  32.301    968
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.42 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.29), residues: 884
  helix:  2.83 (0.26), residues: 392
  sheet: -0.04 (0.38), residues: 184
  loop : -0.83 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP R 173 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.011   0.001   PHE R 289 
 TYR   0.014   0.001   TYR R 199 
 ARG   0.002   0.000   ARG B 137 

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8319 (tp40) cc_final: 0.8000 (tp-100)
REVERT: A  309 GLU cc_start: 0.7774 (pm20) cc_final: 0.7529 (mp0)
REVERT: B   59 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7326 (m-80)
REVERT: B  338 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8260 (mt)
REVERT: R   86 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8571 (m)
  outliers start: 16
  outliers final: 11
  residues processed: 97
  average time/residue: 0.1343
  time to fit residues: 19.2084
Evaluate side-chains
  98 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue   39 VAL
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain R residue  329 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 83 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0970
   chunk 88 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.131920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.112553 restraints weight = 10462.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.115819 restraints weight = 6161.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.118089 restraints weight = 4285.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
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      :  0.003   0.027   6659  Z= 0.182
  Angle     :  0.463   5.591   9111  Z= 0.252
  Chirality :  0.039   0.152   1099
  Planarity :  0.003   0.033   1145
  Dihedral  :  4.277  33.667    968
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.42 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.29), residues: 884
  helix:  2.83 (0.26), residues: 392
  sheet: -0.08 (0.38), residues: 184
  loop : -0.84 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.022   0.001   PHE R  49 
 TYR   0.014   0.001   TYR R 199 
 ARG   0.002   0.000   ARG B 137 

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8326 (tp40) cc_final: 0.8000 (tp-100)
REVERT: A  309 GLU cc_start: 0.7772 (pm20) cc_final: 0.7533 (mp0)
REVERT: B   59 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.7120 (m-80)
REVERT: B  188 MET cc_start: 0.8256 (mmm) cc_final: 0.7850 (mtp)
REVERT: B  338 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8249 (mt)
REVERT: R   86 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8572 (m)
  outliers start: 16
  outliers final: 13
  residues processed: 98
  average time/residue: 0.1356
  time to fit residues: 19.5457
Evaluate side-chains
  101 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue   39 VAL
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain R residue  329 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 75 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
R 299 GLN
R 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.129624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.110291 restraints weight = 10508.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.113530 restraints weight = 6212.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.115791 restraints weight = 4333.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6659  Z= 0.243
  Angle     :  0.487   5.685   9111  Z= 0.267
  Chirality :  0.040   0.150   1099
  Planarity :  0.003   0.033   1145
  Dihedral  :  4.401  33.895    968
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.09 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.29), residues: 884
  helix:  2.71 (0.26), residues: 392
  sheet: -0.16 (0.38), residues: 184
  loop : -0.89 (0.33), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 211 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.013   0.001   PHE R 289 
 TYR   0.016   0.001   TYR R 199 
 ARG   0.002   0.000   ARG B 137 

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

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

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1768 Ramachandran restraints generated.
    884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.760 
Fit side-chains
REVERT: A  267 GLN cc_start: 0.8415 (tp40) cc_final: 0.8126 (tp-100)
REVERT: A  309 GLU cc_start: 0.7723 (pm20) cc_final: 0.7497 (mp0)
REVERT: B   59 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7020 (m-80)
REVERT: B  338 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8277 (mt)
  outliers start: 17
  outliers final: 13
  residues processed: 95
  average time/residue: 0.1384
  time to fit residues: 19.3760
Evaluate side-chains
  97 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue   39 VAL
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  317 VAL
Chi-restraints excluded: chain R residue  329 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0000
   chunk 46 optimal weight:    0.6980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.131225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.111754 restraints weight = 10507.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.115025 restraints weight = 6176.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.117260 restraints weight = 4309.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6659  Z= 0.188
  Angle     :  0.472   5.824   9111  Z= 0.256
  Chirality :  0.039   0.151   1099
  Planarity :  0.003   0.032   1145
  Dihedral  :  4.323  33.908    968
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 17.92 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.28), residues: 884
  helix:  2.77 (0.26), residues: 392
  sheet: -0.12 (0.38), residues: 182
  loop : -0.88 (0.33), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.022   0.001   PHE R  49 
 TYR   0.013   0.001   TYR R 199 
 ARG   0.002   0.000   ARG B 137 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2204.03 seconds
wall clock time: 38 minutes 54.45 seconds (2334.45 seconds total)