Starting phenix.real_space_refine
on Fri Aug 22 18:17:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gg3_29993/08_2025/8gg3_29993.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gg3_29993/08_2025/8gg3_29993.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gg3_29993/08_2025/8gg3_29993.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gg3_29993/08_2025/8gg3_29993.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gg3_29993/08_2025/8gg3_29993.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gg3_29993/08_2025/8gg3_29993.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.031
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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      46      5.16       5
     C    4317      2.51       5
     N    1161      2.21       5
     O    1226      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6753
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1758
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 166
          Unresolved non-hydrogen angles: 199
          Unresolved non-hydrogen dihedrals: 136
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 14, 'ASP:plan': 4, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 114
    Chain: "B"
      Number of atoms: 2439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2439
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 5, 'TRANS': 325}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 105
          Unresolved non-hydrogen angles: 128
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 6, 'GLU:plan': 4, 'ASP:plan': 6, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 87
    Chain: "G"
      Number of atoms: 343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 343
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 62
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 53
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "R"
      Number of atoms: 2160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2160
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 7, 'TRANS': 272}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 93
          Unresolved non-hydrogen angles: 115
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 3, 'HIS:plan': 2, 'ASP:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 55
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 21
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 6}
          Link IDs: {None: 6}
  Time building chain proxies: 1.48, per 1000 atoms: 0.22
  Number of scatterers: 6753
  At special positions: 0
  Unit cell: (85.0346, 133.626, 99.7855, 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      46     16.00
     P       3     15.00
     O    1226      8.00
     N    1161      7.00
     C    4317      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.54
  Conformation dependent library (CDL) restraints added in 375.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1694

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 8 sheets defined
      48.5% alpha, 17.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.564A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ARG A  20 " --> pdb=" O   GLU A  16 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 59
      removed outlier: 3.861A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 237
      removed outlier: 3.772A  pdb=" N   ILE A 235 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.595A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.034A  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: 3.552A  pdb=" N   ARG A 336 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 4.211A  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 24
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 12 through 24
      removed outlier: 3.623A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'R' and resid 34 through 61
      removed outlier: 3.656A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ILE R  43 " --> pdb=" O   VAL R  39 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL R  44 " --> pdb=" O   MET R  40 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 65
      removed outlier: 3.609A  pdb=" N   GLN R  65 " --> pdb=" O   GLU R  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 62 through 65'
    Processing helix  chain 'R' and resid 66 through 86
      removed outlier: 3.540A  pdb=" N   TYR R  70 " --> pdb=" O   THR R  66 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 86 through 97
    Processing helix  chain 'R' and resid 101 through 137
      removed outlier: 4.096A  pdb=" N   TRP R 105 " --> pdb=" O   PHE R 101 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   CYS R 106 " --> pdb=" O   GLY R 102 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   CYS R 125 " --> pdb=" O   ILE R 121 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 4.116A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
      removed outlier: 3.609A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 238
      removed outlier: 5.387A  pdb=" N   VAL R 210 " --> pdb=" O   VAL R 206 " (cutoff:3.500A)
      Proline residue:  R 211  - end of helix
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.801A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.239A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
    Processing helix  chain 'R' and resid 317 through 327
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 338
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.558A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 9.666A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.692A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.673A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.211A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.102A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.818A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.316A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.333A  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: 6.924A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.201A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.645A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.168A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.876A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)

    356 hydrogen bonds defined for protein.
    1035 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: 0.86

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1498
        1.33 -     1.45: 1560
        1.45 -     1.57: 3764
        1.57 -     1.69: 5
        1.69 -     1.81: 64
  Bond restraints: 6891
  Sorted by residual:
  bond pdb=" CA  THR A 325 "
       pdb=" C   THR A 325 "
    ideal  model  delta    sigma   weight residual
    1.526  1.493  0.033 1.15e-02 7.56e+03 8.02e+00
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.450 -0.053 2.00e-02 2.50e+03 7.10e+00
  bond pdb=" CA  ASP A 331 "
       pdb=" C   ASP A 331 "
    ideal  model  delta    sigma   weight residual
    1.528  1.499  0.029 1.18e-02 7.18e+03 6.20e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.441 -0.047 2.00e-02 2.50e+03 5.49e+00
  bond pdb=" C   THR A 335 "
       pdb=" O   THR A 335 "
    ideal  model  delta    sigma   weight residual
    1.237  1.210  0.027 1.17e-02 7.31e+03 5.29e+00
  ... (remaining 6886 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 9279
        1.78 -     3.57: 96
        3.57 -     5.35: 20
        5.35 -     7.14: 5
        7.14 -     8.92: 2
  Bond angle restraints: 9402
  Sorted by residual:
  angle pdb=" C   THR A 325 "
        pdb=" N   PRO A 326 "
        pdb=" CA  PRO A 326 "
      ideal   model   delta    sigma   weight residual
     119.76  113.19    6.57 1.03e+00 9.43e-01 4.07e+01
  angle pdb=" C   THR A 325 "
        pdb=" CA  THR A 325 "
        pdb=" CB  THR A 325 "
      ideal   model   delta    sigma   weight residual
     110.96  107.26    3.70 1.33e+00 5.65e-01 7.73e+00
  angle pdb=" N   GLU A 330 "
        pdb=" CA  GLU A 330 "
        pdb=" C   GLU A 330 "
      ideal   model   delta    sigma   weight residual
     111.00  118.66   -7.66 2.80e+00 1.28e-01 7.49e+00
  angle pdb=" C   ALA A 324 "
        pdb=" N   THR A 325 "
        pdb=" CA  THR A 325 "
      ideal   model   delta    sigma   weight residual
     123.21  119.99    3.22 1.19e+00 7.06e-01 7.30e+00
  angle pdb=" N   PRO A 326 "
        pdb=" CA  PRO A 326 "
        pdb=" C   PRO A 326 "
      ideal   model   delta    sigma   weight residual
     111.14  107.01    4.13 1.56e+00 4.11e-01 7.02e+00
  ... (remaining 9397 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.56: 3623
       16.56 -    33.13: 315
       33.13 -    49.69: 64
       49.69 -    66.25: 7
       66.25 -    82.82: 7
  Dihedral angle restraints: 4016
    sinusoidal: 1409
      harmonic: 2607
  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   21.78   82.82     1      2.00e+01 2.50e-03 2.10e+01
  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 -157.44  -22.56     0      5.00e+00 4.00e-02 2.04e+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  146.15  -76.88     1      2.00e+01 2.50e-03 1.86e+01
  ... (remaining 4013 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 711
       0.032 -    0.064: 265
       0.064 -    0.097: 87
       0.097 -    0.129: 43
       0.129 -    0.161: 4
  Chirality restraints: 1110
  Sorted by residual:
  chirality pdb=" CA  THR A 335 "
            pdb=" N   THR A 335 "
            pdb=" C   THR A 335 "
            pdb=" CB  THR A 335 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.16 2.00e-01 2.50e+01 6.47e-01
  chirality pdb=" CA  GLU A 330 "
            pdb=" N   GLU A 330 "
            pdb=" C   GLU A 330 "
            pdb=" CB  GLU A 330 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.68e-01
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.54   -0.14 2.00e-01 2.50e+01 4.73e-01
  ... (remaining 1107 not shown)

  Planarity restraints: 1177
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 331 "    0.030 5.00e-02 4.00e+02   4.48e-02 3.21e+00
        pdb=" N   PRO A 332 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 332 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 332 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 205 "    0.008 2.00e-02 2.50e+03   1.59e-02 2.53e+00
        pdb=" C   ILE R 205 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   ILE R 205 "    0.010 2.00e-02 2.50e+03
        pdb=" N   VAL R 206 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 335 "    0.007 2.00e-02 2.50e+03   1.50e-02 2.24e+00
        pdb=" C   THR A 335 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   THR A 335 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ARG A 336 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1174 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1038
        2.76 -     3.29: 6104
        3.29 -     3.83: 10512
        3.83 -     4.36: 12069
        4.36 -     4.90: 22569
  Nonbonded interactions: 52292
  Sorted by model distance:
  nonbonded pdb=" O   SER R 111 "
            pdb=" OG  SER R 165 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   TYR R 132 "
            pdb=" OG1 THR R 136 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.319 3.040
  ... (remaining 52287 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.300
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.010
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6892  Z= 0.173
  Angle     :  0.527   8.922   9404  Z= 0.283
  Chirality :  0.041   0.161   1110
  Planarity :  0.003   0.045   1177
  Dihedral  : 13.400  82.815   2319
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.28), residues: 876
  helix:  1.54 (0.26), residues: 397
  sheet:  0.11 (0.40), residues: 165
  loop : -1.02 (0.30), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 175 
 TYR   0.009   0.001   TYR A 339 
 PHE   0.026   0.001   PHE R  49 
 TRP   0.009   0.001   TRP B  99 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6891)
  covalent geometry    : angle       0.52728 ( 9402)
  SS BOND              : bond        0.00026 (    1)
  SS BOND              : angle       0.90766 (    2)
  hydrogen bonds       : bond        0.22917 (  356)
  hydrogen bonds       : angle       6.45233 ( 1035)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.303 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1020
  time to fit residues: 13.4863
Evaluate side-chains
  90 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
B  75 GLN
R 172 HIS
R 296 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.145620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.115747 restraints weight = 8284.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 1.93
r_work: 0.3036 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.1019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6892  Z= 0.144
  Angle     :  0.520   6.487   9404  Z= 0.281
  Chirality :  0.042   0.138   1110
  Planarity :  0.004   0.033   1177
  Dihedral  :  6.185  83.562    985
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  7.22 %
    Favored  : 91.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.28), residues: 876
  helix:  2.01 (0.26), residues: 400
  sheet:  0.36 (0.42), residues: 158
  loop : -1.15 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 131 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.014   0.001   PHE R  49 
 TRP   0.007   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6891)
  covalent geometry    : angle       0.52029 ( 9402)
  SS BOND              : bond        0.00153 (    1)
  SS BOND              : angle       0.86204 (    2)
  hydrogen bonds       : bond        0.06492 (  356)
  hydrogen bonds       : angle       4.53110 ( 1035)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.269 
Fit side-chains
  outliers start: 7
  outliers final: 3
  residues processed: 91
  average time/residue: 0.0868
  time to fit residues: 10.6760
Evaluate side-chains
  85 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 8 optimal weight:    0.1980
   chunk 85 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0020
   chunk 63 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 62 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0770
   chunk 86 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0980
   overall best weight:    0.2146

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
B  75 GLN
R 172 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.133818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.104082 restraints weight = 8491.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 1.92
r_work: 0.2994 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2864 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.1290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   6892  Z= 0.097
  Angle     :  0.442   6.204   9404  Z= 0.239
  Chirality :  0.040   0.136   1110
  Planarity :  0.003   0.033   1177
  Dihedral  :  5.886  81.293    985
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  9.92 %
    Favored  : 89.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.29), residues: 876
  helix:  2.39 (0.26), residues: 398
  sheet:  0.57 (0.42), residues: 158
  loop : -1.12 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 131 
 TYR   0.008   0.001   TYR A 339 
 PHE   0.010   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B 297 
 HIS   0.008   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00169 ( 6891)
  covalent geometry    : angle       0.44215 ( 9402)
  SS BOND              : bond        0.00097 (    1)
  SS BOND              : angle       0.80532 (    2)
  hydrogen bonds       : bond        0.04637 (  356)
  hydrogen bonds       : angle       4.07364 ( 1035)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  368 ASP cc_start: 0.6798 (p0) cc_final: 0.6568 (p0)
REVERT: B   59 TYR cc_start: 0.8394 (m-80) cc_final: 0.7570 (m-80)
  outliers start: 7
  outliers final: 4
  residues processed: 95
  average time/residue: 0.0998
  time to fit residues: 12.1935
Evaluate side-chains
  90 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  243 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 85 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 33 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 56 optimal weight:    7.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
R 296 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.131433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.101422 restraints weight = 8516.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 1.93
r_work: 0.2952 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6892  Z= 0.115
  Angle     :  0.464   6.253   9404  Z= 0.248
  Chirality :  0.040   0.135   1110
  Planarity :  0.003   0.034   1177
  Dihedral  :  5.847  82.510    985
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 11.58 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.28), residues: 876
  helix:  2.47 (0.26), residues: 398
  sheet:  0.59 (0.42), residues: 158
  loop : -1.17 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 131 
 TYR   0.011   0.001   TYR A 318 
 PHE   0.012   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6891)
  covalent geometry    : angle       0.46410 ( 9402)
  SS BOND              : bond        0.00145 (    1)
  SS BOND              : angle       0.75737 (    2)
  hydrogen bonds       : bond        0.04948 (  356)
  hydrogen bonds       : angle       3.99457 ( 1035)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8521 (tp-100) cc_final: 0.8200 (tp40)
REVERT: A  309 GLU cc_start: 0.7416 (pm20) cc_final: 0.7146 (pm20)
REVERT: A  368 ASP cc_start: 0.6844 (p0) cc_final: 0.6618 (p0)
REVERT: A  378 ASP cc_start: 0.8764 (m-30) cc_final: 0.8516 (m-30)
REVERT: B   59 TYR cc_start: 0.8475 (m-80) cc_final: 0.7940 (m-80)
REVERT: B  228 ASP cc_start: 0.8505 (m-30) cc_final: 0.8196 (m-30)
REVERT: B  258 ASP cc_start: 0.8371 (t0) cc_final: 0.8167 (t0)
REVERT: G   38 MET cc_start: 0.7945 (ttp) cc_final: 0.7597 (ttp)
  outliers start: 10
  outliers final: 9
  residues processed: 98
  average time/residue: 0.0927
  time to fit residues: 11.9919
Evaluate side-chains
  97 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 85 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0170
   chunk 45 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 67 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.1824

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.128477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.098217 restraints weight = 8618.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 1.94
r_work: 0.2911 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6892  Z= 0.155
  Angle     :  0.503   6.435   9404  Z= 0.268
  Chirality :  0.042   0.135   1110
  Planarity :  0.003   0.034   1177
  Dihedral  :  5.981  84.216    985
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 13.08 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.28), residues: 876
  helix:  2.39 (0.26), residues: 398
  sheet:  0.54 (0.42), residues: 157
  loop : -1.21 (0.30), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 131 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.013   0.001   PHE B 241 
 TRP   0.009   0.001   TRP B 339 
 HIS   0.014   0.002   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 6891)
  covalent geometry    : angle       0.50328 ( 9402)
  SS BOND              : bond        0.00179 (    1)
  SS BOND              : angle       0.72945 (    2)
  hydrogen bonds       : bond        0.05620 (  356)
  hydrogen bonds       : angle       4.09790 ( 1035)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  309 GLU cc_start: 0.7414 (pm20) cc_final: 0.7130 (pm20)
REVERT: A  368 ASP cc_start: 0.6886 (p0) cc_final: 0.6667 (p0)
REVERT: A  378 ASP cc_start: 0.8777 (m-30) cc_final: 0.8527 (m-30)
REVERT: B   59 TYR cc_start: 0.8599 (m-80) cc_final: 0.8171 (m-80)
REVERT: B  228 ASP cc_start: 0.8598 (m-30) cc_final: 0.8249 (m-30)
REVERT: G   38 MET cc_start: 0.7912 (ttp) cc_final: 0.7550 (ttp)
  outliers start: 9
  outliers final: 9
  residues processed: 97
  average time/residue: 0.0922
  time to fit residues: 11.9516
Evaluate side-chains
  97 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0980
   chunk 53 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
R 296 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.129175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.099452 restraints weight = 8611.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 1.88
r_work: 0.2922 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2789 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6892  Z= 0.135
  Angle     :  0.486   6.487   9404  Z= 0.260
  Chirality :  0.041   0.135   1110
  Planarity :  0.003   0.034   1177
  Dihedral  :  5.914  84.264    985
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 13.53 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.28), residues: 876
  helix:  2.39 (0.26), residues: 398
  sheet:  0.66 (0.42), residues: 156
  loop : -1.26 (0.30), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 131 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.013   0.001   PHE B 241 
 TRP   0.009   0.001   TRP B 339 
 HIS   0.006   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6891)
  covalent geometry    : angle       0.48619 ( 9402)
  SS BOND              : bond        0.00157 (    1)
  SS BOND              : angle       0.81379 (    2)
  hydrogen bonds       : bond        0.05359 (  356)
  hydrogen bonds       : angle       4.05087 ( 1035)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8372 (mmmt) cc_final: 0.7960 (mmtp)
REVERT: A  309 GLU cc_start: 0.7452 (pm20) cc_final: 0.7159 (pm20)
REVERT: A  368 ASP cc_start: 0.6868 (p0) cc_final: 0.6643 (p0)
REVERT: A  378 ASP cc_start: 0.8753 (m-30) cc_final: 0.8498 (m-30)
REVERT: B   59 TYR cc_start: 0.8644 (m-80) cc_final: 0.8415 (m-80)
REVERT: G   38 MET cc_start: 0.7916 (ttp) cc_final: 0.7571 (ttp)
  outliers start: 12
  outliers final: 11
  residues processed: 98
  average time/residue: 0.0852
  time to fit residues: 11.3655
Evaluate side-chains
  99 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 64 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 46 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 78 optimal weight:    0.2980
   chunk 5 optimal weight:    2.9990
   chunk 81 optimal weight:    0.6980
   chunk 77 optimal weight:    0.2980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 294 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.131214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.101179 restraints weight = 8541.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 1.93
r_work: 0.2940 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2806 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6892  Z= 0.107
  Angle     :  0.459   6.401   9404  Z= 0.247
  Chirality :  0.040   0.171   1110
  Planarity :  0.003   0.035   1177
  Dihedral  :  5.823  83.288    985
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.53 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.28), residues: 876
  helix:  2.47 (0.26), residues: 398
  sheet:  0.72 (0.43), residues: 156
  loop : -1.22 (0.30), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 228 
 TYR   0.009   0.001   TYR A 339 
 PHE   0.012   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B 339 
 HIS   0.006   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 6891)
  covalent geometry    : angle       0.45859 ( 9402)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       0.79238 (    2)
  hydrogen bonds       : bond        0.04776 (  356)
  hydrogen bonds       : angle       3.94556 ( 1035)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A  368 ASP cc_start: 0.6760 (p0) cc_final: 0.6539 (p0)
REVERT: B   59 TYR cc_start: 0.8718 (m-80) cc_final: 0.8483 (m-80)
REVERT: B  228 ASP cc_start: 0.8432 (m-30) cc_final: 0.8222 (m-30)
REVERT: G   38 MET cc_start: 0.7864 (ttp) cc_final: 0.7517 (ttp)
  outliers start: 13
  outliers final: 10
  residues processed: 100
  average time/residue: 0.0876
  time to fit residues: 11.8164
Evaluate side-chains
  96 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  165 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 9 optimal weight:    0.0970
   chunk 48 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 60 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
R 296 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.131193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.101142 restraints weight = 8617.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 1.93
r_work: 0.2937 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6892  Z= 0.110
  Angle     :  0.460   6.397   9404  Z= 0.247
  Chirality :  0.040   0.134   1110
  Planarity :  0.003   0.035   1177
  Dihedral  :  5.721  83.374    985
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.29 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.29), residues: 876
  helix:  2.50 (0.26), residues: 398
  sheet:  0.73 (0.43), residues: 156
  loop : -1.21 (0.30), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 131 
 TYR   0.012   0.001   TYR A 318 
 PHE   0.012   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 6891)
  covalent geometry    : angle       0.46017 ( 9402)
  SS BOND              : bond        0.00153 (    1)
  SS BOND              : angle       0.78735 (    2)
  hydrogen bonds       : bond        0.04682 (  356)
  hydrogen bonds       : angle       3.91645 ( 1035)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A  309 GLU cc_start: 0.7365 (pm20) cc_final: 0.7076 (pm20)
REVERT: A  368 ASP cc_start: 0.6751 (p0) cc_final: 0.6497 (p0)
REVERT: A  378 ASP cc_start: 0.8752 (m-30) cc_final: 0.8541 (m-30)
REVERT: B  228 ASP cc_start: 0.8393 (m-30) cc_final: 0.8170 (m-30)
REVERT: B  258 ASP cc_start: 0.8202 (t0) cc_final: 0.8002 (t0)
  outliers start: 12
  outliers final: 12
  residues processed: 97
  average time/residue: 0.0914
  time to fit residues: 11.8816
Evaluate side-chains
  100 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0000
   chunk 68 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 59 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   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 220 HIS
R 296 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.131659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.101704 restraints weight = 8590.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 1.93
r_work: 0.2949 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2816 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   6892  Z= 0.109
  Angle     :  0.460   6.408   9404  Z= 0.247
  Chirality :  0.041   0.183   1110
  Planarity :  0.003   0.035   1177
  Dihedral  :  5.710  83.173    985
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.44 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.29), residues: 876
  helix:  2.50 (0.26), residues: 398
  sheet:  0.76 (0.43), residues: 156
  loop : -1.18 (0.30), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 175 
 TYR   0.009   0.001   TYR A 339 
 PHE   0.012   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B 339 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 6891)
  covalent geometry    : angle       0.45979 ( 9402)
  SS BOND              : bond        0.00151 (    1)
  SS BOND              : angle       0.78746 (    2)
  hydrogen bonds       : bond        0.04654 (  356)
  hydrogen bonds       : angle       3.89378 ( 1035)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  309 GLU cc_start: 0.7333 (pm20) cc_final: 0.7029 (pm20)
REVERT: A  368 ASP cc_start: 0.6762 (p0) cc_final: 0.6523 (p0)
REVERT: A  378 ASP cc_start: 0.8747 (m-30) cc_final: 0.8542 (m-30)
REVERT: B   59 TYR cc_start: 0.8493 (m-80) cc_final: 0.7953 (m-80)
REVERT: B  228 ASP cc_start: 0.8397 (m-30) cc_final: 0.8180 (m-30)
REVERT: G   38 MET cc_start: 0.7877 (ttp) cc_final: 0.7498 (ttp)
  outliers start: 13
  outliers final: 13
  residues processed: 97
  average time/residue: 0.0854
  time to fit residues: 11.1712
Evaluate side-chains
  99 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 87 optimal weight:    0.0970
   chunk 63 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
R 296 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.132174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.102752 restraints weight = 8544.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 1.86
r_work: 0.2968 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.1600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6892  Z= 0.113
  Angle     :  0.466   6.428   9404  Z= 0.250
  Chirality :  0.041   0.134   1110
  Planarity :  0.003   0.035   1177
  Dihedral  :  5.705  83.155    985
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.59 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.33 (0.29), residues: 876
  helix:  2.50 (0.26), residues: 398
  sheet:  0.74 (0.43), residues: 156
  loop : -1.19 (0.30), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 131 
 TYR   0.009   0.001   TYR A 339 
 PHE   0.012   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B 339 
 HIS   0.004   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 6891)
  covalent geometry    : angle       0.46570 ( 9402)
  SS BOND              : bond        0.00162 (    1)
  SS BOND              : angle       0.80158 (    2)
  hydrogen bonds       : bond        0.04668 (  356)
  hydrogen bonds       : angle       3.90654 ( 1035)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  309 GLU cc_start: 0.7345 (pm20) cc_final: 0.7040 (pm20)
REVERT: A  368 ASP cc_start: 0.6798 (p0) cc_final: 0.6564 (p0)
REVERT: A  378 ASP cc_start: 0.8742 (m-30) cc_final: 0.8533 (m-30)
REVERT: B   59 TYR cc_start: 0.8463 (m-80) cc_final: 0.7958 (m-80)
REVERT: B  228 ASP cc_start: 0.8401 (m-30) cc_final: 0.8188 (m-30)
REVERT: G   38 MET cc_start: 0.7891 (ttp) cc_final: 0.7527 (ttp)
  outliers start: 12
  outliers final: 12
  residues processed: 95
  average time/residue: 0.0720
  time to fit residues: 9.2287
Evaluate side-chains
  98 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 67 optimal weight:    6.9990
   chunk 22 optimal weight:    0.4980
   chunk 48 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
R 296 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.131439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.101517 restraints weight = 8518.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 1.92
r_work: 0.2951 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6892  Z= 0.115
  Angle     :  0.468   6.452   9404  Z= 0.251
  Chirality :  0.041   0.182   1110
  Planarity :  0.003   0.035   1177
  Dihedral  :  5.693  83.178    985
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.59 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.29), residues: 876
  helix:  2.49 (0.26), residues: 398
  sheet:  0.73 (0.42), residues: 156
  loop : -1.20 (0.30), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 131 
 TYR   0.009   0.001   TYR A 339 
 PHE   0.012   0.001   PHE B 241 
 TRP   0.008   0.001   TRP B 339 
 HIS   0.003   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 6891)
  covalent geometry    : angle       0.46801 ( 9402)
  SS BOND              : bond        0.00169 (    1)
  SS BOND              : angle       0.81068 (    2)
  hydrogen bonds       : bond        0.04721 (  356)
  hydrogen bonds       : angle       3.91236 ( 1035)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2052.45 seconds
wall clock time: 35 minutes 53.08 seconds (2153.08 seconds total)