Starting phenix.real_space_refine
on Tue Mar 11 15:55:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uo0_42423/03_2025/8uo0_42423.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uo0_42423/03_2025/8uo0_42423.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uo0_42423/03_2025/8uo0_42423.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uo0_42423/03_2025/8uo0_42423.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uo0_42423/03_2025/8uo0_42423.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uo0_42423/03_2025/8uo0_42423.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.019
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      30      5.16       5
     C    4018      2.51       5
     N    1076      2.21       5
     O    1095      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6222
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1595
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 229, 1583
          Classifications: {'peptide': 229}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 88}
          Link IDs: {'PTRANS': 6, 'TRANS': 222}
          Chain breaks: 4
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 336
          Unresolved non-hydrogen angles: 411
          Unresolved non-hydrogen dihedrals: 272
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 13}
          Unresolved non-hydrogen planarities: 219
      Conformer: "B"
        Number of residues, atoms: 229, 1583
          Classifications: {'peptide': 229}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 88}
          Link IDs: {'PTRANS': 6, 'TRANS': 222}
          Chain breaks: 4
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 336
          Unresolved non-hydrogen angles: 411
          Unresolved non-hydrogen dihedrals: 272
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 13}
          Unresolved non-hydrogen planarities: 219
          bond proxies already assigned to first conformer: 1597
    Chain: "B"
      Number of atoms: 2290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2290
          Classifications: {'peptide': 333}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 82}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 270
          Unresolved non-hydrogen angles: 337
          Unresolved non-hydrogen dihedrals: 203
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 6, 'ARG:plan': 10, 'ASN:plan1': 6, 'ASP:plan': 24}
          Unresolved non-hydrogen planarities: 196
    Chain: "G"
      Number of atoms: 327
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 327
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 99
          Unresolved non-hydrogen angles: 118
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 48
    Chain: "R"
      Number of atoms: 1963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 1963
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 96}
          Link IDs: {'PTRANS': 7, 'TRANS': 277}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 344
          Unresolved non-hydrogen angles: 431
          Unresolved non-hydrogen dihedrals: 279
          Unresolved non-hydrogen chiralities: 31
          Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 192
    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: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR A 360 " occ=0.17
      ... (22 atoms not shown)
      pdb=" OH BTYR A 360 " occ=0.83
  Time building chain proxies: 5.96, per 1000 atoms: 0.96
  Number of scatterers: 6222
  At special positions: 0
  Unit cell: (82.4315, 134.493, 98.0501, 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      30     16.00
     P       3     15.00
     O    1095      8.00
     N    1076      7.00
     C    4018      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.70
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1712

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      47.8% alpha, 16.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 40
      removed outlier: 3.764A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   THR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 3.679A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   GLN A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   MET A  60 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   HIS A  64 " --> pdb=" O   MET A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.789A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 278
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.682A  pdb=" N   ALA A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 333 through 352
      removed outlier: 3.525A  pdb=" N   ALA A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   TYR A 339 " --> pdb=" O   THR A 335 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 5 through 26
      removed outlier: 3.634A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.654A  pdb=" N   THR B  34 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 9 through 23
      removed outlier: 3.807A  pdb=" N   LYS G  20 " --> pdb=" O   VAL G  16 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.881A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 30 through 61
      removed outlier: 3.590A  pdb=" N   MET R  36 " --> pdb=" O   TRP R  32 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLY R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE R  47 " --> pdb=" O   ILE R  43 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL R  48 " --> pdb=" O   VAL R  44 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 97
      removed outlier: 4.126A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   SER R  74 " --> pdb=" O   TYR R  70 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.693A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
      removed outlier: 3.846A  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 208
    Processing helix  chain 'R' and resid 208 through 238
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 3.607A  pdb=" N   ILE R 278 " --> pdb=" O   THR R 274 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.817A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.633A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 317 through 327
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 339
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.674A  pdb=" N   THR A 210 " --> pdb=" O   MET A 221 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 7.151A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.143A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   VAL A 287 " --> pdb=" O  ATYR A 360 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 49
      removed outlier: 6.907A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.236A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.390A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.936A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.136A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.378A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.986A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.181A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 4.048A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.497A  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: 6.812A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.988A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.811A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 5.852A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    351 hydrogen bonds defined for protein.
    1026 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.77

  Time building geometry restraints manager: 2.00 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1058
        1.32 -     1.45: 1741
        1.45 -     1.57: 3513
        1.57 -     1.69: 5
        1.69 -     1.81: 39
  Bond restraints: 6356
  Sorted by residual:
  bond pdb=" C   ALA A  18 "
       pdb=" O   ALA A  18 "
    ideal  model  delta    sigma   weight residual
    1.237  1.278 -0.041 1.17e-02 7.31e+03 1.25e+01
  bond pdb=" N   SER A 352 "
       pdb=" CA  SER A 352 "
    ideal  model  delta    sigma   weight residual
    1.454  1.496 -0.043 1.23e-02 6.61e+03 1.22e+01
  bond pdb=" N   VAL A 301 "
       pdb=" CA  VAL A 301 "
    ideal  model  delta    sigma   weight residual
    1.460  1.502 -0.042 1.21e-02 6.83e+03 1.21e+01
  bond pdb=" C   LYS A  58 "
       pdb=" O   LYS A  58 "
    ideal  model  delta    sigma   weight residual
    1.236  1.272 -0.035 1.15e-02 7.56e+03 9.46e+00
  bond pdb=" CA  SER A 275 "
       pdb=" CB  SER A 275 "
    ideal  model  delta    sigma   weight residual
    1.530  1.483  0.047 1.56e-02 4.11e+03 9.00e+00
  ... (remaining 6351 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.67: 8505
        2.67 -     5.34: 196
        5.34 -     8.01: 21
        8.01 -    10.68: 9
       10.68 -    13.34: 3
  Bond angle restraints: 8734
  Sorted by residual:
  angle pdb=" N   PRO A 332 "
        pdb=" CA  PRO A 332 "
        pdb=" C   PRO A 332 "
      ideal   model   delta    sigma   weight residual
     113.53  100.73   12.80 1.39e+00 5.18e-01 8.48e+01
  angle pdb=" N   ASN A  23 "
        pdb=" CA  ASN A  23 "
        pdb=" C   ASN A  23 "
      ideal   model   delta    sigma   weight residual
     111.28  103.13    8.15 1.09e+00 8.42e-01 5.59e+01
  angle pdb=" N   LEU A 270 "
        pdb=" CA  LEU A 270 "
        pdb=" C   LEU A 270 "
      ideal   model   delta    sigma   weight residual
     111.28  104.14    7.14 1.09e+00 8.42e-01 4.29e+01
  angle pdb=" N   GLN A 267 "
        pdb=" CA  GLN A 267 "
        pdb=" C   GLN A 267 "
      ideal   model   delta    sigma   weight residual
     111.28  104.35    6.93 1.09e+00 8.42e-01 4.04e+01
  angle pdb=" N   PRO A 328 "
        pdb=" CA  PRO A 328 "
        pdb=" C   PRO A 328 "
      ideal   model   delta    sigma   weight residual
     111.26  101.71    9.55 1.63e+00 3.76e-01 3.43e+01
  ... (remaining 8729 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.25: 3545
       33.25 -    66.49: 70
       66.49 -    99.74: 0
       99.74 -   132.98: 1
      132.98 -   166.23: 2
  Dihedral angle restraints: 3618
    sinusoidal: 985
      harmonic: 2633
  Sorted by residual:
  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  -96.96  166.23     1      2.00e+01 2.50e-03 4.73e+01
  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  -48.14  152.74     1      2.00e+01 2.50e-03 4.53e+01
  dihedral pdb=" O3B GTP A 401 "
           pdb=" O3A GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PA  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -68.92 -172.61  103.69     1      2.00e+01 2.50e-03 2.97e+01
  ... (remaining 3615 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 759
       0.047 -    0.094: 188
       0.094 -    0.141: 82
       0.141 -    0.189: 35
       0.189 -    0.236: 6
  Chirality restraints: 1070
  Sorted by residual:
  chirality pdb=" CA  GLU A 230 "
            pdb=" N   GLU A 230 "
            pdb=" C   GLU A 230 "
            pdb=" CB  GLU A 230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  ARG A  20 "
            pdb=" N   ARG A  20 "
            pdb=" C   ARG A  20 "
            pdb=" CB  ARG A  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CA  ILE G   9 "
            pdb=" N   ILE G   9 "
            pdb=" C   ILE G   9 "
            pdb=" CB  ILE G   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 1067 not shown)

  Planarity restraints: 1095
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 333 "   -0.233 9.50e-02 1.11e+02   1.05e-01 6.71e+00
        pdb=" NE  ARG A 333 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 333 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 333 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 333 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  28 "   -0.012 2.00e-02 2.50e+03   2.49e-02 6.21e+00
        pdb=" C   LYS A  28 "    0.043 2.00e-02 2.50e+03
        pdb=" O   LYS A  28 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   GLN A  29 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  29 "   -0.012 2.00e-02 2.50e+03   2.45e-02 6.01e+00
        pdb=" C   GLN A  29 "    0.042 2.00e-02 2.50e+03
        pdb=" O   GLN A  29 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LEU A  30 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1092 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1580
        2.79 -     3.32: 5825
        3.32 -     3.85: 9667
        3.85 -     4.37: 10099
        4.37 -     4.90: 18574
  Nonbonded interactions: 45745
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B  83 "
            pdb=" OG1 THR B  86 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   LEU A 272 "
            pdb=" OG  SER A 275 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" N   GLN B 259 "
            pdb=" OE1 GLN B 259 "
     model   vdw
     2.312 3.120
  nonbonded pdb=" O   VAL R  34 "
            pdb=" N   GLY R  37 "
     model   vdw
     2.327 3.120
  nonbonded pdb=" O   ILE B  37 "
            pdb=" NZ  LYS B 301 "
     model   vdw
     2.338 3.120
  ... (remaining 45740 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.17 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:          0.240
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.350
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
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      :  0.006   0.054   6356  Z= 0.394
  Angle     :  0.928  13.344   8734  Z= 0.634
  Chirality :  0.057   0.236   1070
  Planarity :  0.005   0.105   1095
  Dihedral  : 13.945 166.231   1903
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.62 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.29), residues: 885
  helix:  2.48 (0.27), residues: 373
  sheet:  0.36 (0.39), residues: 184
  loop : -0.93 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 332 
 HIS   0.009   0.001   HIS R 296 
 PHE   0.011   0.001   PHE R 104 
 TYR   0.034   0.002   TYR R 185 
 ARG   0.004   0.000   ARG A 389 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.663 
Fit side-chains
REVERT: A  267 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8269 (tp40)
REVERT: B  110 ASN cc_start: 0.9283 (m-40) cc_final: 0.8919 (m110)
REVERT: R  161 SER cc_start: 0.8939 (t) cc_final: 0.8470 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1669
  time to fit residues: 22.9717
Evaluate side-chains
  76 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 22 optimal weight:   20.0000
   chunk 44 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 = 0.3696 r_free = 0.3696 target = 0.124979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.097198 restraints weight = 35481.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.101350 restraints weight = 11258.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.104177 restraints weight = 5976.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3426
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3426
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6356  Z= 0.244
  Angle     :  0.524   6.477   8734  Z= 0.289
  Chirality :  0.041   0.137   1070
  Planarity :  0.003   0.033   1095
  Dihedral  :  9.011 154.274    972
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 10.27 %
    Favored  : 87.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.28), residues: 885
  helix:  2.33 (0.26), residues: 399
  sheet:  0.18 (0.40), residues: 175
  loop : -1.13 (0.31), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.012   0.001   PHE R 104 
 TYR   0.024   0.001   TYR R 185 
 ARG   0.003   0.000   ARG A 389 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.671 
Fit side-chains
REVERT: A  267 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7862 (tp40)
  outliers start: 12
  outliers final: 11
  residues processed: 82
  average time/residue: 0.1588
  time to fit residues: 18.1154
Evaluate side-chains
  84 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  307 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0470
   chunk 14 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.7278

-------------------------------------------------------------------------------
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 = 0.3675 r_free = 0.3675 target = 0.124916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.096817 restraints weight = 43137.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.102042 restraints weight = 14540.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.105032 restraints weight = 6252.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3404
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3404 r_free = 0.3404    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3404 r_free = 0.3404    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3404
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6356  Z= 0.148
  Angle     :  0.449   6.408   8734  Z= 0.249
  Chirality :  0.039   0.134   1070
  Planarity :  0.003   0.030   1095
  Dihedral  :  8.561 149.261    972
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 14.17 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.29), residues: 885
  helix:  2.79 (0.26), residues: 392
  sheet:  0.18 (0.39), residues: 181
  loop : -1.07 (0.32), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 211 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.009   0.001   PHE B 241 
 TYR   0.023   0.001   TYR R 185 
 ARG   0.004   0.000   ARG A 231 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.740 
Fit side-chains
REVERT: A  267 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7814 (tp40)
  outliers start: 4
  outliers final: 4
  residues processed: 81
  average time/residue: 0.1493
  time to fit residues: 17.2312
Evaluate side-chains
  80 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  307 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 2 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 82 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 87 optimal weight:    0.5980
   chunk 55 optimal weight:    9.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
R  69 ASN
** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.125240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.098514 restraints weight = 44344.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.102703 restraints weight = 14081.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.105989 restraints weight = 6302.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3443
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3443
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6356  Z= 0.193
  Angle     :  0.474   6.313   8734  Z= 0.259
  Chirality :  0.040   0.132   1070
  Planarity :  0.003   0.031   1095
  Dihedral  :  8.315 147.360    972
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 13.96 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.28), residues: 885
  helix:  2.88 (0.26), residues: 392
  sheet:  0.07 (0.38), residues: 181
  loop : -1.19 (0.31), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.025   0.001   TYR R 185 
 ARG   0.003   0.000   ARG A 231 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.745 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8229 (ttmm) cc_final: 0.7805 (mmtt)
REVERT: B   58 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8628 (pt)
  outliers start: 20
  outliers final: 15
  residues processed: 85
  average time/residue: 0.1548
  time to fit residues: 18.4573
Evaluate side-chains
  90 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  104 PHE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  171 MET
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  307 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 52 optimal weight:    7.9990
   chunk 47 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0570
   chunk 2 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    1.1702

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

Flipped N/Q/H residues before XYZ refinement:
B 225 HIS
** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.125494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.098038 restraints weight = 39345.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.102728 restraints weight = 12431.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.106825 restraints weight = 5816.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3452
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3452
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6356  Z= 0.189
  Angle     :  0.463   6.103   8734  Z= 0.254
  Chirality :  0.040   0.142   1070
  Planarity :  0.003   0.030   1095
  Dihedral  :  8.061 145.581    972
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.22 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.28), residues: 885
  helix:  2.98 (0.26), residues: 391
  sheet:  0.12 (0.38), residues: 186
  loop : -1.17 (0.31), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 277 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.025   0.001   TYR R 185 
 ARG   0.005   0.000   ARG A 231 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.654 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8298 (ttmm) cc_final: 0.7746 (mmtt)
REVERT: B   58 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8625 (pt)
REVERT: R  174 TYR cc_start: 0.8339 (p90) cc_final: 0.8102 (p90)
  outliers start: 14
  outliers final: 13
  residues processed: 87
  average time/residue: 0.1583
  time to fit residues: 18.9540
Evaluate side-chains
  86 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  104 PHE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0670
   chunk 4 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 25 optimal weight:    9.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.0122

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

Flipped N/Q/H residues before XYZ refinement:
** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.125784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.098103 restraints weight = 33730.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.102263 restraints weight = 10921.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.105104 restraints weight = 5864.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3445
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3445 r_free = 0.3445    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3445 r_free = 0.3445    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3445
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6356  Z= 0.171
  Angle     :  0.458   5.958   8734  Z= 0.251
  Chirality :  0.040   0.146   1070
  Planarity :  0.003   0.030   1095
  Dihedral  :  7.805 143.668    972
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 16.02 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.29), residues: 885
  helix:  3.02 (0.26), residues: 391
  sheet:  0.03 (0.37), residues: 193
  loop : -1.09 (0.32), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 277 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.031   0.001   TYR R 185 
 ARG   0.004   0.000   ARG A 231 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.665 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8333 (ttmm) cc_final: 0.7792 (mmtt)
REVERT: B   58 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8663 (pt)
REVERT: B  234 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8626 (m-80)
  outliers start: 22
  outliers final: 18
  residues processed: 89
  average time/residue: 0.1492
  time to fit residues: 18.7853
Evaluate side-chains
  93 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  332 TRP
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  104 PHE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  171 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  294 ILE
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  307 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 55 optimal weight:    0.0980
   chunk 87 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   chunk 50 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 60 optimal weight:   20.0000
   chunk 58 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 76 optimal weight:    0.6980
   chunk 75 optimal weight:    8.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.127087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.099333 restraints weight = 51477.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.103684 restraints weight = 15354.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.107758 restraints weight = 6669.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3466
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3466 r_free = 0.3466    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3466 r_free = 0.3466    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3466
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6356  Z= 0.141
  Angle     :  0.437   5.826   8734  Z= 0.240
  Chirality :  0.039   0.156   1070
  Planarity :  0.003   0.029   1095
  Dihedral  :  7.487 140.809    972
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 16.84 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.29), residues: 885
  helix:  2.98 (0.26), residues: 397
  sheet:  0.23 (0.38), residues: 182
  loop : -1.04 (0.32), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 277 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.009   0.001   PHE B 199 
 TYR   0.026   0.001   TYR R 174 
 ARG   0.001   0.000   ARG A 389 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.697 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8280 (ttmm) cc_final: 0.7877 (mmtt)
REVERT: B   58 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8621 (pt)
REVERT: B  234 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8585 (m-80)
REVERT: R  185 TYR cc_start: 0.7153 (m-80) cc_final: 0.6607 (m-80)
  outliers start: 21
  outliers final: 18
  residues processed: 89
  average time/residue: 0.1401
  time to fit residues: 18.1054
Evaluate side-chains
  92 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  332 TRP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  104 PHE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  171 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  307 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   chunk 18 optimal weight:    0.0570
   chunk 3 optimal weight:    0.0980
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.128956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.101534 restraints weight = 37785.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.106109 restraints weight = 12709.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.109839 restraints weight = 5945.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3499
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3499 r_free = 0.3499    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3499 r_free = 0.3499    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3499
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6356  Z= 0.119
  Angle     :  0.422   5.694   8734  Z= 0.229
  Chirality :  0.039   0.165   1070
  Planarity :  0.002   0.028   1095
  Dihedral  :  7.088 136.120    972
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 17.45 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.29), residues: 885
  helix:  3.02 (0.26), residues: 398
  sheet:  0.29 (0.37), residues: 188
  loop : -0.94 (0.33), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 277 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.008   0.001   PHE B 199 
 TYR   0.019   0.001   TYR R 174 
 ARG   0.001   0.000   ARG A 389 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.737 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8291 (ttmm) cc_final: 0.7935 (mmtt)
REVERT: B   58 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8628 (pt)
REVERT: B  234 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8556 (m-80)
  outliers start: 19
  outliers final: 16
  residues processed: 95
  average time/residue: 0.1394
  time to fit residues: 19.2036
Evaluate side-chains
  96 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  332 TRP
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  104 PHE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  171 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  307 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 48 optimal weight:    0.4980
   chunk 63 optimal weight:    7.9990
   chunk 27 optimal weight:    0.7980
   chunk 87 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
R  51 ASN
** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.129297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.102209 restraints weight = 40235.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.107644 restraints weight = 12146.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.109818 restraints weight = 5346.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3509
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3509 r_free = 0.3509    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3509 r_free = 0.3509    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3509
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6356  Z= 0.140
  Angle     :  0.441   6.086   8734  Z= 0.239
  Chirality :  0.040   0.158   1070
  Planarity :  0.003   0.029   1095
  Dihedral  :  6.973 132.830    972
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 17.45 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.29), residues: 885
  helix:  3.03 (0.26), residues: 399
  sheet:  0.13 (0.38), residues: 179
  loop : -0.93 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 277 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.019   0.001   TYR R 174 
 ARG   0.001   0.000   ARG A 389 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.742 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8328 (ttmm) cc_final: 0.7816 (mmtt)
REVERT: B   58 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8722 (pt)
REVERT: B  234 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8623 (m-80)
  outliers start: 21
  outliers final: 19
  residues processed: 88
  average time/residue: 0.1406
  time to fit residues: 17.9832
Evaluate side-chains
  96 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  332 TRP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  104 PHE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  171 MET
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  295 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  307 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 79 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 13 optimal weight:    0.2980
   chunk 50 optimal weight:    0.3980
   chunk 25 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.129635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.102362 restraints weight = 39288.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.107495 restraints weight = 11771.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.110428 restraints weight = 5476.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3513
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3513
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6356  Z= 0.134
  Angle     :  0.438   5.760   8734  Z= 0.238
  Chirality :  0.039   0.166   1070
  Planarity :  0.003   0.029   1095
  Dihedral  :  6.875 128.350    972
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 17.45 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.29), residues: 885
  helix:  3.07 (0.26), residues: 398
  sheet:  0.15 (0.38), residues: 179
  loop : -0.95 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 277 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.009   0.001   PHE B 199 
 TYR   0.018   0.001   TYR R 174 
 ARG   0.001   0.000   ARG A 389 

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8306 (ttmm) cc_final: 0.7812 (mmtt)
REVERT: B   58 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8709 (pt)
REVERT: B  234 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8620 (m-80)
  outliers start: 23
  outliers final: 19
  residues processed: 87
  average time/residue: 0.1358
  time to fit residues: 17.1838
Evaluate side-chains
  96 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  332 TRP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  104 PHE
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  295 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  307 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 84 optimal weight:    0.6980
   chunk 73 optimal weight:    0.3980
   chunk 54 optimal weight:    4.9990
   chunk 38 optimal weight:    0.4980
   chunk 27 optimal weight:    2.9990
   chunk 37 optimal weight:    0.4980
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.130584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.102400 restraints weight = 39703.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.107655 restraints weight = 12457.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.109441 restraints weight = 6237.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3509
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3509 r_free = 0.3509    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3509 r_free = 0.3509    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3509
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6356  Z= 0.124
  Angle     :  0.430   5.936   8734  Z= 0.233
  Chirality :  0.039   0.164   1070
  Planarity :  0.002   0.029   1095
  Dihedral  :  6.277 117.268    972
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 18.69 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.29), residues: 885
  helix:  3.10 (0.26), residues: 399
  sheet:  0.24 (0.37), residues: 190
  loop : -0.92 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 277 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.008   0.001   PHE B 241 
 TYR   0.017   0.001   TYR R 174 
 ARG   0.002   0.000   ARG A 389 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2484.86 seconds
wall clock time: 43 minutes 28.65 seconds (2608.65 seconds total)