Starting phenix.real_space_refine
on Sat Apr  4 23:32:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9odg_70358/04_2026/9odg_70358.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9odg_70358/04_2026/9odg_70358.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9odg_70358/04_2026/9odg_70358.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9odg_70358/04_2026/9odg_70358.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9odg_70358/04_2026/9odg_70358.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9odg_70358/04_2026/9odg_70358.map"
  }
  resolution = 4.3
  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=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      16      5.16       5
     C    3649      2.51       5
     N    1086      2.21       5
     O    1088      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5842
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 322, 1959
          Classifications: {'peptide': 322}
          Incomplete info: {'truncation_to_alanine': 192}
          Link IDs: {'PTRANS': 4, 'TRANS': 317}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 643
          Unresolved non-hydrogen angles: 796
          Unresolved non-hydrogen dihedrals: 502
          Unresolved non-hydrogen chiralities: 59
          Planarities with less than four sites: {'GLU:plan': 23, 'ASP:plan': 21, 'ARG:plan': 15, 'ASN:plan1': 12, 'GLN:plan1': 11, 'PHE:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 341
    Chain: "B"
      Number of atoms: 2150
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2150
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 147}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 435
          Unresolved non-hydrogen angles: 544
          Unresolved non-hydrogen dihedrals: 328
          Unresolved non-hydrogen chiralities: 44
          Planarities with less than four sites: {'ASP:plan': 23, 'GLN:plan1': 10, 'ARG:plan': 14, 'GLU:plan': 7, 'ASN:plan1': 8, 'HIS:plan': 1, 'ASN%COO:plan1': 1}
          Unresolved non-hydrogen planarities: 239
    Chain: "C"
      Number of atoms: 315
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 315
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 92
          Unresolved non-hydrogen angles: 112
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 48
    Chain: "R"
      Number of atoms: 1386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 1386
          Classifications: {'peptide': 279}
          Incomplete info: {'truncation_to_alanine': 253}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 268}
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 907
          Unresolved non-hydrogen angles: 1184
          Unresolved non-hydrogen dihedrals: 768
          Unresolved non-hydrogen chiralities: 112
          Planarities with less than four sites: {'TYR:plan': 14, 'PHE:plan': 18, 'ASN:plan1': 14, 'ARG:plan': 11, 'ASP:plan': 7, 'GLN:plan1': 3, 'TRP:plan': 6, 'HIS:plan': 4, 'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 426
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.54, per 1000 atoms: 0.26
  Number of scatterers: 5842
  At special positions: 0
  Unit cell: (75.84, 101.76, 135.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      16     16.00
     P       3     15.00
     O    1088      8.00
     N    1086      7.00
     C    3649      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.46
  Conformation dependent library (CDL) restraints added in 459.8 milliseconds
  

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1884

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      48.6% alpha, 14.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 31
      removed outlier: 4.088A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 56
      removed outlier: 3.874A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 88
      removed outlier: 3.648A  pdb=" N   TYR A  74 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ARG A  86 " --> pdb=" O   ILE A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 111
    Processing helix  chain 'A' and resid 120 through 133
      removed outlier: 3.644A  pdb=" N   ALA A 124 " --> pdb=" O   THR A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 143
    Processing helix  chain 'A' and resid 150 through 158
      removed outlier: 4.261A  pdb=" N   TYR A 154 " --> pdb=" O   ASP A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 163
    Processing helix  chain 'A' and resid 170 through 176
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 4.520A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 216
      No H-bonds generated for 'chain 'A' and resid 214 through 216'
    Processing helix  chain 'A' and resid 241 through 253
    Processing helix  chain 'A' and resid 271 through 279
      removed outlier: 4.419A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.730A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 311
      removed outlier: 3.749A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ASN A 311 " --> pdb=" O   PHE A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.919A  pdb=" N   ALA A 338 " --> pdb=" O   PHE A 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 25
    Processing helix  chain 'B' and resid 29 through 33
    Processing helix  chain 'C' and resid 10 through 24
    Processing helix  chain 'C' and resid 29 through 45
      removed outlier: 3.691A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ASP C  36 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LEU C  37 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   MET C  38 " --> pdb=" O   ALA C  34 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 48
      No H-bonds generated for 'chain 'C' and resid 46 through 48'
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 3.916A  pdb=" N   THR R  70 " --> pdb=" O   VAL R  66 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL R  78 " --> pdb=" O   LEU R  74 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   CYS R  79 " --> pdb=" O   TYR R  75 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 101 through 130
      removed outlier: 3.532A  pdb=" N   ILE R 105 " --> pdb=" O   THR R 101 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   TYR R 106 " --> pdb=" O   ALA R 102 " (cutoff:3.500A)
      Proline residue:  R 122  - end of helix
      removed outlier: 3.981A  pdb=" N   SER R 125 " --> pdb=" O   LEU R 121 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   VAL R 126 " --> pdb=" O   PRO R 122 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ASN R 127 " --> pdb=" O   PHE R 123 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   TYR R 128 " --> pdb=" O   GLN R 124 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 171
      removed outlier: 4.088A  pdb=" N   LYS R 141 " --> pdb=" O   ASN R 137 " (cutoff:3.500A)
      removed outlier: 4.901A  pdb=" N   ILE R 142 " --> pdb=" O   ILE R 138 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   PHE R 152 " --> pdb=" O   TYR R 148 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 179
      removed outlier: 4.060A  pdb=" N   ASP R 177 " --> pdb=" O   VAL R 173 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 180 through 205
      Proline residue:  R 201  - end of helix
    Processing helix  chain 'R' and resid 224 through 241
      removed outlier: 4.143A  pdb=" N   GLU R 229 " --> pdb=" O   THR R 225 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   ASN R 230 " --> pdb=" O   TRP R 226 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU R 231 " --> pdb=" O   TYR R 227 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU R 232 " --> pdb=" O   TRP R 228 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LYS R 233 " --> pdb=" O   GLU R 229 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 242 through 260
      removed outlier: 3.661A  pdb=" N   VAL R 250 " --> pdb=" O   LEU R 246 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   TYR R 252 " --> pdb=" O   ILE R 248 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 268 through 306
      Proline residue:  R 295  - end of helix
      removed outlier: 3.906A  pdb=" N   VAL R 300 " --> pdb=" O   ILE R 296 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE R 301 " --> pdb=" O   HIS R 297 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 313 through 339
      removed outlier: 3.583A  pdb=" N   ASN R 328 " --> pdb=" O   LEU R 324 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   SER R 329 " --> pdb=" O   GLY R 325 " (cutoff:3.500A)
      Proline residue:  R 333  - end of helix
      removed outlier: 3.531A  pdb=" N   PHE R 338 " --> pdb=" O   VAL R 334 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU R 339 " --> pdb=" O   LEU R 335 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 7.082A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.236A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 226
      removed outlier: 3.841A  pdb=" N   ASN A 269 " --> pdb=" O   VAL A 225 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51
      removed outlier: 3.624A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.632A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ALA B  73 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.694A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.540A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.897A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.870A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA B 167 " --> pdb=" O   THR B 159 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 191
      removed outlier: 4.466A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.880A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 277
      removed outlier: 3.959A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 315 through 320
      removed outlier: 3.506A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)

    387 hydrogen bonds defined for protein.
    1140 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.68

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2086
        1.34 -     1.46: 1108
        1.46 -     1.57: 2711
        1.57 -     1.69: 5
        1.69 -     1.81: 20
  Bond restraints: 5930
  Sorted by residual:
  bond pdb=" N   LYS A  46 "
       pdb=" CA  LYS A  46 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.025 1.19e-02 7.06e+03 4.57e+00
  bond pdb=" CA  GLY B 116 "
       pdb=" C   GLY B 116 "
    ideal  model  delta    sigma   weight residual
    1.514  1.502  0.012 1.41e-02 5.03e+03 7.74e-01
  bond pdb=" CA  PHE A 199 "
       pdb=" C   PHE A 199 "
    ideal  model  delta    sigma   weight residual
    1.522  1.532 -0.010 1.18e-02 7.18e+03 6.96e-01
  bond pdb=" CA  ASP B  83 "
       pdb=" CB  ASP B  83 "
    ideal  model  delta    sigma   weight residual
    1.532  1.519  0.013 1.58e-02 4.01e+03 6.55e-01
  bond pdb=" CA  SER A 228 "
       pdb=" C   SER A 228 "
    ideal  model  delta    sigma   weight residual
    1.531  1.522  0.009 1.12e-02 7.97e+03 6.29e-01
  ... (remaining 5925 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 7950
        1.65 -     3.31: 216
        3.31 -     4.96: 27
        4.96 -     6.61: 8
        6.61 -     8.27: 4
  Bond angle restraints: 8205
  Sorted by residual:
  angle pdb=" C   ASP B 333 "
        pdb=" N   SER B 334 "
        pdb=" CA  SER B 334 "
      ideal   model   delta    sigma   weight residual
     121.54  128.84   -7.30 1.91e+00 2.74e-01 1.46e+01
  angle pdb=" N   ILE B  33 "
        pdb=" CA  ILE B  33 "
        pdb=" C   ILE B  33 "
      ideal   model   delta    sigma   weight residual
     111.77  108.30    3.47 1.04e+00 9.25e-01 1.12e+01
  angle pdb=" C   ALA B  60 "
        pdb=" N   MET B  61 "
        pdb=" CA  MET B  61 "
      ideal   model   delta    sigma   weight residual
     121.89  127.57   -5.68 1.74e+00 3.30e-01 1.07e+01
  angle pdb=" N   GLU A 145 "
        pdb=" CA  GLU A 145 "
        pdb=" C   GLU A 145 "
      ideal   model   delta    sigma   weight residual
     114.56  110.42    4.14 1.27e+00 6.20e-01 1.06e+01
  angle pdb=" N   THR B 164 "
        pdb=" CA  THR B 164 "
        pdb=" CB  THR B 164 "
      ideal   model   delta    sigma   weight residual
     113.65  108.90    4.75 1.47e+00 4.63e-01 1.04e+01
  ... (remaining 8200 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.00: 3358
       33.00 -    66.00: 19
       66.00 -    99.01: 3
       99.01 -   132.01: 0
      132.01 -   165.01: 2
  Dihedral angle restraints: 3382
    sinusoidal: 496
      harmonic: 2886
  Sorted by residual:
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -60.42  165.01     1      2.00e+01 2.50e-03 4.72e+01
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27  -74.49  143.76     1      2.00e+01 2.50e-03 4.34e+01
  dihedral pdb=" O3A GTP A 401 "
           pdb=" O3B GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PG  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.21 -143.95   87.74     1      2.00e+01 2.50e-03 2.31e+01
  ... (remaining 3379 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 586
       0.029 -    0.058: 291
       0.058 -    0.087: 101
       0.087 -    0.116: 42
       0.116 -    0.146: 8
  Chirality restraints: 1028
  Sorted by residual:
  chirality pdb=" CA  LYS A  46 "
            pdb=" N   LYS A  46 "
            pdb=" C   LYS A  46 "
            pdb=" CB  LYS A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.30e-01
  chirality pdb=" CA  ILE B 273 "
            pdb=" N   ILE B 273 "
            pdb=" C   ILE B 273 "
            pdb=" CB  ILE B 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.89e-01
  chirality pdb=" CA  ILE B  81 "
            pdb=" N   ILE B  81 "
            pdb=" C   ILE B  81 "
            pdb=" CB  ILE B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.35e-01
  ... (remaining 1025 not shown)

  Planarity restraints: 1104
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B  60 "    0.007 2.00e-02 2.50e+03   1.52e-02 2.32e+00
        pdb=" C   ALA B  60 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ALA B  60 "    0.010 2.00e-02 2.50e+03
        pdb=" N   MET B  61 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  48 "   -0.023 5.00e-02 4.00e+02   3.54e-02 2.01e+00
        pdb=" N   PRO C  49 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO C  49 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C  49 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 164 "    0.021 5.00e-02 4.00e+02   3.15e-02 1.59e+00
        pdb=" N   PRO A 165 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 165 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 165 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1101 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 2096
        2.84 -     3.35: 5376
        3.35 -     3.87: 8891
        3.87 -     4.38: 8849
        4.38 -     4.90: 15679
  Nonbonded interactions: 40891
  Sorted by model distance:
  nonbonded pdb=" O   SER R 268 "
            pdb=" N   LYS R 271 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" ND2 ASN B 230 "
            pdb=" OD1 ASP B 246 "
     model   vdw
     2.363 3.120
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     2.373 3.040
  nonbonded pdb=" N   TRP R 133 "
            pdb=" O   ILE R 215 "
     model   vdw
     2.387 3.120
  nonbonded pdb=" O   TYR B 145 "
            pdb=" N   GLY B 162 "
     model   vdw
     2.442 3.120
  ... (remaining 40886 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.440
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.010
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6715
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      :  0.002   0.025   5930  Z= 0.149
  Angle     :  0.672   8.268   8205  Z= 0.413
  Chirality :  0.041   0.146   1028
  Planarity :  0.003   0.035   1104
  Dihedral  : 11.350 165.008   1498
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.80 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.28), residues: 974
  helix:  1.75 (0.27), residues: 424
  sheet: -1.98 (0.38), residues: 180
  loop : -1.67 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  96 
 TYR   0.010   0.001   TYR B 289 
 PHE   0.012   0.001   PHE B 234 
 TRP   0.019   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 5930)
  covalent geometry    : angle       0.67229 ( 8205)
  hydrogen bonds       : bond        0.18582 (  387)
  hydrogen bonds       : angle       6.91120 ( 1140)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: B  118 ASP cc_start: 0.8334 (p0) cc_final: 0.8105 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0598
  time to fit residues: 9.0243
Evaluate side-chains
  69 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0770
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0040
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:   40.0000
   overall best weight:    1.5554

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
B 225 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.082900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.068516 restraints weight = 42604.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.069792 restraints weight = 27684.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.070719 restraints weight = 20043.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.071397 restraints weight = 15624.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.071839 restraints weight = 12869.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5930  Z= 0.121
  Angle     :  0.520   6.579   8205  Z= 0.282
  Chirality :  0.042   0.171   1028
  Planarity :  0.003   0.033   1104
  Dihedral  :  8.192 164.100   1028
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.54 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.29), residues: 974
  helix:  2.24 (0.26), residues: 438
  sheet: -1.41 (0.40), residues: 172
  loop : -1.78 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 251 
 TYR   0.015   0.001   TYR A 155 
 PHE   0.028   0.002   PHE A 267 
 TRP   0.022   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 5930)
  covalent geometry    : angle       0.52016 ( 8205)
  hydrogen bonds       : bond        0.03080 (  387)
  hydrogen bonds       : angle       4.55571 ( 1140)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 TYR cc_start: 0.7918 (m-80) cc_final: 0.7331 (m-80)
REVERT: A  223 PHE cc_start: 0.8006 (t80) cc_final: 0.7190 (t80)
REVERT: A  250 PHE cc_start: 0.9096 (t80) cc_final: 0.8460 (t80)
REVERT: A  296 TYR cc_start: 0.8327 (p90) cc_final: 0.7723 (t80)
REVERT: B   58 ILE cc_start: 0.9244 (mm) cc_final: 0.9031 (mm)
REVERT: B   82 TRP cc_start: 0.7232 (m-10) cc_final: 0.6695 (m-10)
REVERT: B  118 ASP cc_start: 0.9036 (p0) cc_final: 0.8741 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0459
  time to fit residues: 5.7215
Evaluate side-chains
  68 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 52 optimal weight:    8.9990
   chunk 49 optimal weight:    0.3980
   chunk 2 optimal weight:   20.0000
   chunk 47 optimal weight:    0.7980
   chunk 36 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   chunk 72 optimal weight:   30.0000
   chunk 30 optimal weight:    4.9990
   chunk 75 optimal weight:   40.0000
   chunk 1 optimal weight:   20.0000
   chunk 43 optimal weight:    0.2980
   overall best weight:    1.8984

-------------------------------------------------------------------------------
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 = 0.3689 r_free = 0.3689 target = 0.079587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.065319 restraints weight = 42908.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.066521 restraints weight = 27907.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.067440 restraints weight = 20196.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.068078 restraints weight = 15782.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.068535 restraints weight = 13026.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.3398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5930  Z= 0.122
  Angle     :  0.517   8.914   8205  Z= 0.277
  Chirality :  0.042   0.138   1028
  Planarity :  0.003   0.033   1104
  Dihedral  :  7.957 161.014   1028
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.62 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  4.27 %
    Favored  : 95.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.29), residues: 974
  helix:  2.51 (0.26), residues: 437
  sheet: -1.07 (0.42), residues: 170
  loop : -1.63 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  49 
 TYR   0.014   0.001   TYR B 264 
 PHE   0.022   0.002   PHE A 267 
 TRP   0.024   0.002   TRP B 169 
 HIS   0.004   0.002   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 5930)
  covalent geometry    : angle       0.51660 ( 8205)
  hydrogen bonds       : bond        0.03097 (  387)
  hydrogen bonds       : angle       4.16930 ( 1140)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 PHE cc_start: 0.8118 (t80) cc_final: 0.7402 (t80)
REVERT: A  227 LEU cc_start: 0.8717 (tt) cc_final: 0.8444 (tt)
REVERT: A  250 PHE cc_start: 0.9206 (t80) cc_final: 0.8612 (t80)
REVERT: A  296 TYR cc_start: 0.8154 (p90) cc_final: 0.7495 (t80)
REVERT: B   82 TRP cc_start: 0.6829 (m-10) cc_final: 0.6049 (m-10)
REVERT: B  118 ASP cc_start: 0.9113 (p0) cc_final: 0.8769 (p0)
  outliers start: 1
  outliers final: 1
  residues processed: 79
  average time/residue: 0.0439
  time to fit residues: 5.2056
Evaluate side-chains
  62 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 70 optimal weight:   50.0000
   chunk 73 optimal weight:    7.9990
   chunk 91 optimal weight:   30.0000
   chunk 80 optimal weight:   40.0000
   chunk 72 optimal weight:    8.9990
   chunk 56 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 74 optimal weight:   20.0000
   chunk 13 optimal weight:    5.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.072559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.058637 restraints weight = 44198.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.059839 restraints weight = 28312.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.060597 restraints weight = 20312.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.061230 restraints weight = 15991.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.061545 restraints weight = 13226.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.5536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   5930  Z= 0.266
  Angle     :  0.685   8.556   8205  Z= 0.383
  Chirality :  0.046   0.188   1028
  Planarity :  0.004   0.037   1104
  Dihedral  :  8.451 161.301   1028
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.88 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.68 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.28), residues: 974
  helix:  1.94 (0.25), residues: 441
  sheet: -1.12 (0.41), residues: 164
  loop : -1.98 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  49 
 TYR   0.032   0.003   TYR A 167 
 PHE   0.023   0.003   PHE C  61 
 TRP   0.032   0.004   TRP B  63 
 HIS   0.006   0.002   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 ( 5930)
  covalent geometry    : angle       0.68457 ( 8205)
  hydrogen bonds       : bond        0.04859 (  387)
  hydrogen bonds       : angle       5.13845 ( 1140)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
REVERT: B  101 MET cc_start: 0.9124 (mmm) cc_final: 0.8709 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0439
  time to fit residues: 4.5413
Evaluate side-chains
  51 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 32 optimal weight:   40.0000
   chunk 57 optimal weight:   10.0000
   chunk 42 optimal weight:    8.9990
   chunk 48 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 41 optimal weight:    4.9990
   chunk 4 optimal weight:    8.9990
   chunk 13 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 225 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.072444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.058545 restraints weight = 44448.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.059721 restraints weight = 28496.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.060550 restraints weight = 20394.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.061155 restraints weight = 15812.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.061574 restraints weight = 13063.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.6082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   5930  Z= 0.227
  Angle     :  0.608   7.062   8205  Z= 0.335
  Chirality :  0.044   0.168   1028
  Planarity :  0.003   0.037   1104
  Dihedral  :  8.223 163.590   1028
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.37 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.29), residues: 974
  helix:  1.96 (0.26), residues: 449
  sheet: -1.12 (0.41), residues: 161
  loop : -2.02 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  49 
 TYR   0.014   0.002   TYR B  59 
 PHE   0.025   0.003   PHE A 307 
 TRP   0.017   0.002   TRP B 169 
 HIS   0.009   0.002   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 5930)
  covalent geometry    : angle       0.60767 ( 8205)
  hydrogen bonds       : bond        0.03924 (  387)
  hydrogen bonds       : angle       4.73393 ( 1140)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.162 
Fit side-chains
REVERT: B  101 MET cc_start: 0.9179 (mmm) cc_final: 0.8815 (mmm)
REVERT: B  111 TYR cc_start: 0.8897 (m-80) cc_final: 0.8672 (m-80)
REVERT: B  150 ARG cc_start: 0.8146 (mmt180) cc_final: 0.7839 (mmt180)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0522
  time to fit residues: 4.7524
Evaluate side-chains
  51 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 69 optimal weight:    5.9990
   chunk 33 optimal weight:   20.0000
   chunk 8 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 11 optimal weight:   40.0000
   chunk 29 optimal weight:    0.8980
   chunk 7 optimal weight:   20.0000
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  57 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.072494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.058459 restraints weight = 43322.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.059606 restraints weight = 27875.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.060421 restraints weight = 20117.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.060918 restraints weight = 15695.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.061387 restraints weight = 13179.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.6350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5930  Z= 0.185
  Angle     :  0.568   6.733   8205  Z= 0.311
  Chirality :  0.044   0.163   1028
  Planarity :  0.003   0.037   1104
  Dihedral  :  8.115 164.159   1028
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.29 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.29), residues: 974
  helix:  2.03 (0.25), residues: 456
  sheet: -1.03 (0.41), residues: 167
  loop : -2.10 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  49 
 TYR   0.014   0.002   TYR B 289 
 PHE   0.024   0.002   PHE A 267 
 TRP   0.022   0.002   TRP B 169 
 HIS   0.008   0.002   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 5930)
  covalent geometry    : angle       0.56799 ( 8205)
  hydrogen bonds       : bond        0.03773 (  387)
  hydrogen bonds       : angle       4.54563 ( 1140)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.212 
Fit side-chains
REVERT: B  101 MET cc_start: 0.9211 (mmm) cc_final: 0.8866 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0388
  time to fit residues: 3.9683
Evaluate side-chains
  51 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 9 optimal weight:   30.0000
   chunk 83 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 11 optimal weight:   20.0000
   chunk 43 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0470
   chunk 58 optimal weight:    5.9990
   chunk 32 optimal weight:   40.0000
   chunk 5 optimal weight:   20.0000
   chunk 47 optimal weight:    6.9990
   overall best weight:    4.8086

-------------------------------------------------------------------------------
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 = 0.3508 r_free = 0.3508 target = 0.070330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.056528 restraints weight = 44698.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.057611 restraints weight = 28679.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.058398 restraints weight = 20754.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.058871 restraints weight = 16217.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.059336 restraints weight = 13698.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.7094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   5930  Z= 0.253
  Angle     :  0.658   9.259   8205  Z= 0.365
  Chirality :  0.045   0.186   1028
  Planarity :  0.003   0.038   1104
  Dihedral  :  8.578 167.459   1028
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.83 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.28), residues: 974
  helix:  1.71 (0.25), residues: 456
  sheet: -0.96 (0.42), residues: 162
  loop : -2.33 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  49 
 TYR   0.017   0.003   TYR B  59 
 PHE   0.026   0.003   PHE A 267 
 TRP   0.023   0.003   TRP B 169 
 HIS   0.009   0.003   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 ( 5930)
  covalent geometry    : angle       0.65830 ( 8205)
  hydrogen bonds       : bond        0.04571 (  387)
  hydrogen bonds       : angle       4.94003 ( 1140)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.156 
Fit side-chains
REVERT: B  101 MET cc_start: 0.9190 (mmm) cc_final: 0.8874 (mmm)
REVERT: B  118 ASP cc_start: 0.9258 (p0) cc_final: 0.9012 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0494
  time to fit residues: 4.4136
Evaluate side-chains
  52 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 80 optimal weight:   40.0000
   chunk 73 optimal weight:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.071749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.057837 restraints weight = 43955.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.058922 restraints weight = 27983.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.059746 restraints weight = 20206.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.060286 restraints weight = 15751.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.060749 restraints weight = 13116.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.7251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5930  Z= 0.170
  Angle     :  0.561   7.334   8205  Z= 0.304
  Chirality :  0.043   0.156   1028
  Planarity :  0.003   0.038   1104
  Dihedral  :  8.374 166.383   1028
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.08 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.29), residues: 974
  helix:  2.22 (0.25), residues: 447
  sheet: -0.88 (0.41), residues: 170
  loop : -2.14 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  49 
 TYR   0.016   0.002   TYR B  59 
 PHE   0.024   0.002   PHE A 267 
 TRP   0.025   0.002   TRP B 169 
 HIS   0.008   0.002   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 5930)
  covalent geometry    : angle       0.56131 ( 8205)
  hydrogen bonds       : bond        0.03557 (  387)
  hydrogen bonds       : angle       4.42801 ( 1140)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.165 
Fit side-chains
REVERT: B  101 MET cc_start: 0.9175 (mmm) cc_final: 0.8828 (mmm)
REVERT: B  118 ASP cc_start: 0.9264 (p0) cc_final: 0.8922 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0435
  time to fit residues: 4.3078
Evaluate side-chains
  52 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 77 optimal weight:    0.2980
   chunk 84 optimal weight:   30.0000
   chunk 41 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 3 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 0 optimal weight:   40.0000
   chunk 47 optimal weight:    4.9990
   overall best weight:    2.6588

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.072037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.058082 restraints weight = 43583.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.059209 restraints weight = 27920.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.059997 restraints weight = 20127.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.060575 restraints weight = 15740.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.060868 restraints weight = 13050.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.7414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5930  Z= 0.149
  Angle     :  0.546   7.395   8205  Z= 0.290
  Chirality :  0.043   0.165   1028
  Planarity :  0.003   0.037   1104
  Dihedral  :  8.298 166.719   1028
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.49 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.29), residues: 974
  helix:  2.54 (0.25), residues: 447
  sheet: -0.91 (0.41), residues: 164
  loop : -2.18 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  49 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.024   0.002   PHE A 267 
 TRP   0.024   0.002   TRP B 169 
 HIS   0.008   0.002   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 5930)
  covalent geometry    : angle       0.54564 ( 8205)
  hydrogen bonds       : bond        0.03304 (  387)
  hydrogen bonds       : angle       4.16664 ( 1140)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.183 
Fit side-chains
REVERT: B  101 MET cc_start: 0.9127 (mmm) cc_final: 0.8853 (mmm)
REVERT: B  118 ASP cc_start: 0.9172 (p0) cc_final: 0.8789 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0431
  time to fit residues: 4.3197
Evaluate side-chains
  54 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 29 optimal weight:    0.2980
   chunk 10 optimal weight:    0.0570
   chunk 71 optimal weight:   30.0000
   chunk 40 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 82 optimal weight:   30.0000
   chunk 50 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 88 optimal weight:    0.8980
   overall best weight:    1.2502

-------------------------------------------------------------------------------
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 = 0.3584 r_free = 0.3584 target = 0.074050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.059946 restraints weight = 43286.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.061115 restraints weight = 27716.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.061868 restraints weight = 19920.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.062494 restraints weight = 15664.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.062972 restraints weight = 12928.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.7379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5930  Z= 0.093
  Angle     :  0.503   8.057   8205  Z= 0.259
  Chirality :  0.042   0.150   1028
  Planarity :  0.002   0.036   1104
  Dihedral  :  7.991 166.049   1028
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.13 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.29), residues: 974
  helix:  2.88 (0.26), residues: 447
  sheet: -0.69 (0.41), residues: 165
  loop : -2.17 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  48 
 TYR   0.010   0.001   TYR A  69 
 PHE   0.022   0.001   PHE A 267 
 TRP   0.027   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00181 ( 5930)
  covalent geometry    : angle       0.50345 ( 8205)
  hydrogen bonds       : bond        0.02600 (  387)
  hydrogen bonds       : angle       3.77758 ( 1140)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.145 
Fit side-chains
REVERT: B  101 MET cc_start: 0.9102 (mmm) cc_final: 0.8880 (mmm)
REVERT: B  118 ASP cc_start: 0.9108 (p0) cc_final: 0.8700 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0425
  time to fit residues: 4.7064
Evaluate side-chains
  55 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 2 optimal weight:   20.0000
   chunk 47 optimal weight:    2.9990
   chunk 56 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9980
   chunk 33 optimal weight:   20.0000
   chunk 54 optimal weight:    2.9990
   chunk 71 optimal weight:   30.0000
   chunk 36 optimal weight:   20.0000
   chunk 51 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 = 0.3552 r_free = 0.3552 target = 0.072458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.058524 restraints weight = 43420.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.059615 restraints weight = 27833.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.060347 restraints weight = 20106.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.060946 restraints weight = 15916.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.061342 restraints weight = 13214.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.7544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5930  Z= 0.143
  Angle     :  0.533   7.460   8205  Z= 0.284
  Chirality :  0.043   0.161   1028
  Planarity :  0.003   0.044   1104
  Dihedral  :  8.160 166.794   1028
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.29 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.29), residues: 974
  helix:  2.91 (0.25), residues: 448
  sheet: -1.03 (0.40), residues: 169
  loop : -2.13 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  49 
 TYR   0.012   0.001   TYR C  40 
 PHE   0.024   0.002   PHE A 267 
 TRP   0.019   0.002   TRP B 169 
 HIS   0.007   0.002   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 5930)
  covalent geometry    : angle       0.53301 ( 8205)
  hydrogen bonds       : bond        0.03099 (  387)
  hydrogen bonds       : angle       3.90762 ( 1140)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1012.25 seconds
wall clock time: 17 minutes 58.81 seconds (1078.81 seconds total)