Starting phenix.real_space_refine
on Tue Mar 11 19:13:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8unp_42412/03_2025/8unp_42412.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8unp_42412/03_2025/8unp_42412.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8unp_42412/03_2025/8unp_42412.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8unp_42412/03_2025/8unp_42412.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8unp_42412/03_2025/8unp_42412.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8unp_42412/03_2025/8unp_42412.cif"
  }
  resolution = 3.3
  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=   0.027
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      43      5.16       5
     C    4225      2.51       5
     N    1130      2.21       5
     O    1158      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6559
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1724
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 237, 1712
          Classifications: {'peptide': 237}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 69}
          Link IDs: {'PTRANS': 5, 'TRANS': 231}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 266
          Unresolved non-hydrogen angles: 323
          Unresolved non-hydrogen dihedrals: 209
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 15, 'ARG:plan': 12, 'ASN:plan1': 3, 'ASP:plan': 10}
          Unresolved non-hydrogen planarities: 191
      Conformer: "B"
        Number of residues, atoms: 237, 1712
          Classifications: {'peptide': 237}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 69}
          Link IDs: {'PTRANS': 5, 'TRANS': 231}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 266
          Unresolved non-hydrogen angles: 323
          Unresolved non-hydrogen dihedrals: 209
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 15, 'ARG:plan': 12, 'ASN:plan1': 3, 'ASP:plan': 10}
          Unresolved non-hydrogen planarities: 191
          bond proxies already assigned to first conformer: 1731
    Chain: "B"
      Number of atoms: 2357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2357
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 5, 'TRANS': 325}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 187
          Unresolved non-hydrogen angles: 229
          Unresolved non-hydrogen dihedrals: 145
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 12}
          Unresolved non-hydrogen planarities: 144
    Chain: "G"
      Number of atoms: 335
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 335
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 85
          Unresolved non-hydrogen angles: 102
          Unresolved non-hydrogen dihedrals: 70
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 43
    Chain: "R"
      Number of atoms: 2095
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2095
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 57}
          Link IDs: {'PTRANS': 7, 'TRANS': 276}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 197
          Unresolved non-hydrogen angles: 247
          Unresolved non-hydrogen dihedrals: 156
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 6, 'GLU:plan': 8, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 108
    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: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR A 360 " occ=0.51
      ... (22 atoms not shown)
      pdb=" OH BTYR A 360 " occ=0.49
  Time building chain proxies: 5.57, per 1000 atoms: 0.85
  Number of scatterers: 6559
  At special positions: 0
  Unit cell: (84.1669, 133.626, 96.3147, 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      43     16.00
     P       3     15.00
     O    1158      8.00
     N    1130      7.00
     C    4225      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: 2.09
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1720

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 8 sheets defined
      47.6% alpha, 17.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 40
      removed outlier: 3.540A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 4.037A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.842A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.115A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 3.572A  pdb=" N   ARG A 317 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.635A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG A 336 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.384A  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 7 through 26
      removed outlier: 4.208A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   LEU B  14 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 10 through 24
      removed outlier: 3.683A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU G  19 " --> pdb=" O   LEU G  15 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.699A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.569A  pdb=" N   LEU R  45 " --> pdb=" O   SER R  41 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA R  46 " --> pdb=" O   LEU R  42 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE R  58 " --> pdb=" O   VAL R  54 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 97
      removed outlier: 4.071A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR R  73 " --> pdb=" O   ASN R  69 " (cutoff:3.500A)
      removed outlier: 4.374A  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 120
    Processing helix  chain 'R' and resid 121 through 137
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 164
      removed outlier: 3.829A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 171
      removed outlier: 3.719A  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
      removed outlier: 3.703A  pdb=" N   SER R 204 " --> pdb=" O   ALA R 200 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 238
      removed outlier: 3.729A  pdb=" N   VAL R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   MET R 215 " --> pdb=" O   PRO R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 3.854A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.376A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 3.590A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      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 208 through 214
      removed outlier: 7.218A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.283A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.074A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.487A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.735A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLY B 330 " --> pdb=" O   CYS B 317 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.859A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL B  71 " --> pdb=" O   HIS B  62 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.097A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.038A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.747A  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: 6.941A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.844A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.891A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.936A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 5.022A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)

    348 hydrogen bonds defined for protein.
    1020 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.09

  Time building geometry restraints manager: 2.24 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1303
        1.33 -     1.45: 1701
        1.45 -     1.57: 3635
        1.57 -     1.69: 5
        1.69 -     1.81: 59
  Bond restraints: 6703
  Sorted by residual:
  bond pdb=" CA  GLN A  12 "
       pdb=" C   GLN A  12 "
    ideal  model  delta    sigma   weight residual
    1.523  1.452  0.071 1.41e-02 5.03e+03 2.53e+01
  bond pdb=" CA  ASP A 223 "
       pdb=" C   ASP A 223 "
    ideal  model  delta    sigma   weight residual
    1.523  1.468  0.055 1.23e-02 6.61e+03 1.98e+01
  bond pdb=" CA  THR A 325 "
       pdb=" C   THR A 325 "
    ideal  model  delta    sigma   weight residual
    1.523  1.468  0.055 1.24e-02 6.50e+03 1.98e+01
  bond pdb=" C5  GTP A 401 "
       pdb=" C6  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.477 -0.087 2.00e-02 2.50e+03 1.89e+01
  bond pdb=" C4  GTP A 401 "
       pdb=" C5  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.469 -0.079 2.00e-02 2.50e+03 1.54e+01
  ... (remaining 6698 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.87: 9050
        2.87 -     5.74: 110
        5.74 -     8.61: 9
        8.61 -    11.49: 6
       11.49 -    14.36: 2
  Bond angle restraints: 9177
  Sorted by residual:
  angle pdb=" N   GLN A  12 "
        pdb=" CA  GLN A  12 "
        pdb=" C   GLN A  12 "
      ideal   model   delta    sigma   weight residual
     113.16   99.62   13.54 1.24e+00 6.50e-01 1.19e+02
  angle pdb=" N   ARG A 228 "
        pdb=" CA  ARG A 228 "
        pdb=" C   ARG A 228 "
      ideal   model   delta    sigma   weight residual
     110.10  124.46  -14.36 1.49e+00 4.50e-01 9.28e+01
  angle pdb=" N   ILE R  58 "
        pdb=" CA  ILE R  58 "
        pdb=" C   ILE R  58 "
      ideal   model   delta    sigma   weight residual
     110.62  101.44    9.18 1.02e+00 9.61e-01 8.09e+01
  angle pdb=" N   THR A 263 "
        pdb=" CA  THR A 263 "
        pdb=" C   THR A 263 "
      ideal   model   delta    sigma   weight residual
     110.53  100.96    9.57 1.32e+00 5.74e-01 5.26e+01
  angle pdb=" N   ARG A 231 "
        pdb=" CA  ARG A 231 "
        pdb=" C   ARG A 231 "
      ideal   model   delta    sigma   weight residual
     110.23  100.03   10.20 1.45e+00 4.76e-01 4.95e+01
  ... (remaining 9172 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.82: 3801
       33.82 -    67.63: 48
       67.63 -   101.45: 1
      101.45 -   135.27: 2
      135.27 -   169.08: 3
  Dihedral angle restraints: 3855
    sinusoidal: 1208
      harmonic: 2647
  Sorted by residual:
  dihedral pdb=" O5' GTP A 401 "
           pdb=" O3A GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" PB  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     274.12  105.04  169.08     1      2.00e+01 2.50e-03 4.76e+01
  dihedral pdb=" C4' GTP A 401 "
           pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     260.87  100.64  160.23     1      2.00e+01 2.50e-03 4.66e+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
     291.08  152.69  138.39     1      2.00e+01 2.50e-03 4.19e+01
  ... (remaining 3852 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 819
       0.044 -    0.088: 206
       0.088 -    0.132: 70
       0.132 -    0.176: 7
       0.176 -    0.219: 1
  Chirality restraints: 1103
  Sorted by residual:
  chirality pdb=" CA  ARG A 228 "
            pdb=" N   ARG A 228 "
            pdb=" C   ARG A 228 "
            pdb=" CB  ARG A 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  VAL R  44 "
            pdb=" N   VAL R  44 "
            pdb=" C   VAL R  44 "
            pdb=" CB  VAL R  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.76e-01
  chirality pdb=" CA  ILE R  58 "
            pdb=" N   ILE R  58 "
            pdb=" C   ILE R  58 "
            pdb=" CB  ILE R  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.65e-01
  ... (remaining 1100 not shown)

  Planarity restraints: 1145
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 320 "    0.053 5.00e-02 4.00e+02   8.08e-02 1.04e+01
        pdb=" N   PRO A 321 "   -0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO A 321 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 321 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R  42 "    0.013 2.00e-02 2.50e+03   2.48e-02 6.16e+00
        pdb=" C   LEU R  42 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   LEU R  42 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ILE R  43 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R  33 "   -0.012 2.00e-02 2.50e+03   2.42e-02 5.85e+00
        pdb=" C   VAL R  33 "    0.042 2.00e-02 2.50e+03
        pdb=" O   VAL R  33 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   VAL R  34 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1142 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 804
        2.75 -     3.28: 6231
        3.28 -     3.82: 10286
        3.82 -     4.36: 11339
        4.36 -     4.90: 20929
  Nonbonded interactions: 49589
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  55 "
            pdb=" O2A GTP A 401 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" N   GLN A  12 "
            pdb=" N   ARG A  13 "
     model   vdw
     2.246 2.560
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OD1 ASN A 239 "
            pdb=" NZ  LYS B  57 "
     model   vdw
     2.307 3.120
  ... (remaining 49584 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=0.49 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.820
  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:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     21.350
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:3.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
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   0.087   6703  Z= 0.382
  Angle     :  0.795  14.357   9177  Z= 0.502
  Chirality :  0.044   0.219   1103
  Planarity :  0.004   0.081   1145
  Dihedral  : 13.788 169.085   2132
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  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:  0.82 (0.29), residues: 889
  helix:  1.96 (0.27), residues: 400
  sheet:  0.16 (0.40), residues: 171
  loop : -1.06 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP R 313 
 HIS   0.010   0.001   HIS A 220 
 PHE   0.018   0.001   PHE A 222 
 TYR   0.019   0.001   TYR B  59 
 ARG   0.002   0.000   ARG R 175 

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.668 
Fit side-chains
REVERT: A  267 GLN cc_start: 0.8277 (tp-100) cc_final: 0.7739 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.2340
  time to fit residues: 28.5665
Evaluate side-chains
  72 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:   20.0000
   chunk 45 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
A 220 HIS
A 254 ASN
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 241 HIS
R 322 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.124241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.097583 restraints weight = 31545.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 4.25
r_work: 0.3049 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3041
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3041 r_free = 0.3041    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3041 r_free = 0.3041    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3041
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.1047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6703  Z= 0.208
  Angle     :  0.516   7.209   9177  Z= 0.276
  Chirality :  0.042   0.159   1103
  Planarity :  0.003   0.040   1145
  Dihedral  : 10.628 178.686    990
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  8.22 %
    Favored  : 90.75 %
  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:  1.04 (0.29), residues: 889
  helix:  2.12 (0.26), residues: 410
  sheet:  0.08 (0.39), residues: 180
  loop : -0.94 (0.33), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 339 
 HIS   0.006   0.001   HIS R 241 
 PHE   0.016   0.001   PHE R  61 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.002   0.000   ARG A  42 

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A  267 GLN cc_start: 0.8124 (tp-100) cc_final: 0.7670 (tp-100)
REVERT: A  311 TYR cc_start: 0.8360 (m-80) cc_final: 0.8152 (m-80)
  outliers start: 6
  outliers final: 4
  residues processed: 80
  average time/residue: 0.1755
  time to fit residues: 19.1814
Evaluate side-chains
  76 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain R residue  143 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 74 optimal weight:    0.5980
   chunk 44 optimal weight:    0.2980
   chunk 82 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 80 optimal weight:    0.8980
   chunk 50 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0670
   chunk 19 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
R 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.125837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.098000 restraints weight = 43308.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 5.40
r_work: 0.3011 rms_B_bonded: 5.31 restraints_weight: 2.0000
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2999
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2999 r_free = 0.2999    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2999 r_free = 0.2999    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2999
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   6703  Z= 0.130
  Angle     :  0.459   7.478   9177  Z= 0.243
  Chirality :  0.040   0.163   1103
  Planarity :  0.003   0.037   1145
  Dihedral  : 10.338 179.654    990
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 10.27 %
    Favored  : 89.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: 889
  helix:  2.41 (0.26), residues: 404
  sheet:  0.13 (0.39), residues: 181
  loop : -1.00 (0.33), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 297 
 HIS   0.006   0.001   HIS R 241 
 PHE   0.010   0.001   PHE A 212 
 TYR   0.008   0.001   TYR B  59 
 ARG   0.001   0.000   ARG A 389 

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.723 
Fit side-chains
REVERT: A  267 GLN cc_start: 0.7950 (tp-100) cc_final: 0.7517 (tp-100)
REVERT: B  155 ASN cc_start: 0.7969 (t0) cc_final: 0.7729 (t0)
  outliers start: 3
  outliers final: 2
  residues processed: 84
  average time/residue: 0.1838
  time to fit residues: 21.2281
Evaluate side-chains
  76 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  349 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0970
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 241 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.124759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.097422 restraints weight = 35046.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 4.82
r_work: 0.3008 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3005
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3005
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6703  Z= 0.143
  Angle     :  0.458   7.632   9177  Z= 0.239
  Chirality :  0.040   0.170   1103
  Planarity :  0.003   0.036   1145
  Dihedral  : 10.185 178.143    990
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 11.82 %
    Favored  : 86.30 %
  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:  1.35 (0.29), residues: 889
  helix:  2.53 (0.27), residues: 404
  sheet:  0.22 (0.40), residues: 181
  loop : -0.95 (0.33), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 339 
 HIS   0.006   0.001   HIS R 241 
 PHE   0.009   0.001   PHE A 212 
 TYR   0.014   0.001   TYR B  59 
 ARG   0.001   0.000   ARG G  27 

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.694 
Fit side-chains
REVERT: B  259 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8478 (pt0)
  outliers start: 11
  outliers final: 4
  residues processed: 90
  average time/residue: 0.1772
  time to fit residues: 21.6486
Evaluate side-chains
  81 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain R residue  143 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 35 optimal weight:    0.3980
   chunk 88 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0570
   chunk 13 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
R 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.125178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.097429 restraints weight = 32571.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 4.48
r_work: 0.3029 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3026
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3026
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6703  Z= 0.135
  Angle     :  0.452   7.573   9177  Z= 0.235
  Chirality :  0.040   0.179   1103
  Planarity :  0.003   0.036   1145
  Dihedral  : 10.146 178.993    990
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 13.36 %
    Favored  : 85.10 %
  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:  1.44 (0.29), residues: 889
  helix:  2.57 (0.27), residues: 404
  sheet:  0.29 (0.40), residues: 181
  loop : -0.89 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 339 
 HIS   0.006   0.001   HIS R 241 
 PHE   0.009   0.001   PHE A 212 
 TYR   0.013   0.001   TYR B  59 
 ARG   0.006   0.000   ARG R 221 

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.703 
Fit side-chains
  outliers start: 9
  outliers final: 4
  residues processed: 84
  average time/residue: 0.1725
  time to fit residues: 20.0100
Evaluate side-chains
  75 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  143 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 26 optimal weight:    0.3980
   chunk 59 optimal weight:    1.9990
   chunk 37 optimal weight:    0.2980
   chunk 85 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0070
   chunk 68 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.5200

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

Flipped N/Q/H residues before XYZ refinement:
R 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.126010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.098690 restraints weight = 27850.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 4.16
r_work: 0.3041 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3050
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3050
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6703  Z= 0.126
  Angle     :  0.445   7.492   9177  Z= 0.232
  Chirality :  0.040   0.184   1103
  Planarity :  0.003   0.036   1145
  Dihedral  : 10.098 178.873    990
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.87 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.29), residues: 889
  helix:  2.53 (0.27), residues: 405
  sheet:  0.29 (0.40), residues: 181
  loop : -0.80 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 211 
 HIS   0.006   0.001   HIS R 241 
 PHE   0.009   0.001   PHE R 217 
 TYR   0.010   0.001   TYR B  59 
 ARG   0.004   0.000   ARG R 221 

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.815 
Fit side-chains
REVERT: B  259 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8482 (pt0)
  outliers start: 10
  outliers final: 6
  residues processed: 82
  average time/residue: 0.1847
  time to fit residues: 20.8176
Evaluate side-chains
  78 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   15 LEU
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  236 SER
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
R 241 HIS
R 322 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.122481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.095035 restraints weight = 31102.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 4.31
r_work: 0.2986 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2992
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2992 r_free = 0.2992    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2992 r_free = 0.2992    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2992
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6703  Z= 0.201
  Angle     :  0.482   7.681   9177  Z= 0.253
  Chirality :  0.041   0.195   1103
  Planarity :  0.003   0.036   1145
  Dihedral  : 10.128 178.565    990
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.04 %
    Favored  : 83.90 %
  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:  1.41 (0.29), residues: 889
  helix:  2.47 (0.27), residues: 410
  sheet:  0.16 (0.39), residues: 188
  loop : -0.76 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 211 
 HIS   0.007   0.001   HIS R 241 
 PHE   0.010   0.001   PHE R 101 
 TYR   0.016   0.001   TYR B  59 
 ARG   0.005   0.000   ARG R 221 

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.770 
Fit side-chains
REVERT: B  259 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8502 (pt0)
  outliers start: 12
  outliers final: 11
  residues processed: 86
  average time/residue: 0.1753
  time to fit residues: 20.7747
Evaluate side-chains
  87 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   15 LEU
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  236 SER
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 85 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 84 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
R 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.121531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.095510 restraints weight = 35353.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 4.58
r_work: 0.2992 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3002
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3002
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6703  Z= 0.273
  Angle     :  0.516   7.782   9177  Z= 0.272
  Chirality :  0.042   0.199   1103
  Planarity :  0.003   0.037   1145
  Dihedral  : 10.225 178.357    990
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 2.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.38 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.11 (0.29), residues: 889
  helix:  2.16 (0.27), residues: 418
  sheet:  0.13 (0.39), residues: 186
  loop : -0.99 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 241 
 PHE   0.012   0.001   PHE R 101 
 TYR   0.018   0.001   TYR B  59 
 ARG   0.003   0.000   ARG R 221 

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.766 
Fit side-chains
REVERT: B  259 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8547 (pt0)
  outliers start: 14
  outliers final: 11
  residues processed: 86
  average time/residue: 0.1615
  time to fit residues: 19.3228
Evaluate side-chains
  86 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   15 LEU
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  236 SER
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 26 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 33 optimal weight:    0.2980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
R 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.124211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.097782 restraints weight = 42524.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 5.09
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3211
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3211
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6703  Z= 0.148
  Angle     :  0.462   7.601   9177  Z= 0.241
  Chirality :  0.040   0.189   1103
  Planarity :  0.003   0.038   1145
  Dihedral  : 10.138 178.268    990
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.24 %
    Favored  : 82.88 %
  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:  1.29 (0.29), residues: 889
  helix:  2.39 (0.27), residues: 410
  sheet:  0.14 (0.39), residues: 180
  loop : -0.88 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 241 
 PHE   0.008   0.001   PHE A 212 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.004   0.000   ARG R 221 

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.707 
Fit side-chains
REVERT: A  349 SER cc_start: 0.8999 (p) cc_final: 0.8787 (p)
REVERT: B  259 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8399 (pt0)
  outliers start: 11
  outliers final: 9
  residues processed: 88
  average time/residue: 0.1676
  time to fit residues: 20.4797
Evaluate side-chains
  88 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   15 LEU
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  236 SER
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0030
   overall best weight:    0.8992

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

Flipped N/Q/H residues before XYZ refinement:
R 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.124090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.098531 restraints weight = 24846.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 3.78
r_work: 0.3080 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3070
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3070
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6703  Z= 0.168
  Angle     :  0.470   8.494   9177  Z= 0.245
  Chirality :  0.040   0.200   1103
  Planarity :  0.003   0.037   1145
  Dihedral  : 10.107 177.545    990
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.41 %
    Favored  : 82.53 %
  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:  1.36 (0.29), residues: 889
  helix:  2.41 (0.27), residues: 411
  sheet:  0.13 (0.38), residues: 186
  loop : -0.79 (0.35), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 339 
 HIS   0.006   0.001   HIS R 241 
 PHE   0.008   0.001   PHE A 212 
 TYR   0.011   0.001   TYR B  59 
 ARG   0.004   0.000   ARG R 221 

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.754 
Fit side-chains
REVERT: A  294 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8305 (mm110)
REVERT: A  349 SER cc_start: 0.9058 (OUTLIER) cc_final: 0.8802 (p)
REVERT: B  234 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.7926 (t80)
REVERT: B  259 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8533 (pt0)
  outliers start: 12
  outliers final: 9
  residues processed: 86
  average time/residue: 0.1778
  time to fit residues: 21.0674
Evaluate side-chains
  89 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   15 LEU
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  236 SER
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 4 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 87 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 5 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
R 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.121997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.096380 restraints weight = 25952.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 3.82
r_work: 0.3047 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3039
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3039
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   6703  Z= 0.246
  Angle     :  0.505   8.733   9177  Z= 0.265
  Chirality :  0.041   0.199   1103
  Planarity :  0.003   0.037   1145
  Dihedral  : 10.162 177.131    990
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 15.75 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.23 (0.29), residues: 889
  helix:  2.33 (0.26), residues: 410
  sheet:  0.07 (0.38), residues: 186
  loop : -0.87 (0.34), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 241 
 PHE   0.010   0.001   PHE R 289 
 TYR   0.017   0.001   TYR B  59 
 ARG   0.003   0.000   ARG R 221 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3776.14 seconds
wall clock time: 65 minutes 34.31 seconds (3934.31 seconds total)