Starting phenix.real_space_refine
on Tue Feb 11 19:45:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8unp_42412/02_2025/8unp_42412.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8unp_42412/02_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_42412/02_2025/8unp_42412.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8unp_42412/02_2025/8unp_42412.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8unp_42412/02_2025/8unp_42412.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8unp_42412/02_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-5592/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: 5.48, per 1000 atoms: 0.84
  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: 1.79
  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: 0.70
  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: 1.92

  Time building geometry restraints manager: 2.05 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:             1.950
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.810
  Find NCS groups from input model:        0.090
  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:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.320
-------------------------------------------------------------------------------
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  : 0.782 
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: 0.2302
  time to fit residues: 28.1584
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  : 0.679 
-------------------------------------------------------------------------------
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 = 0.124200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.097522 restraints weight = 31550.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 4.26
r_work: 0.3047 rms_B_bonded: 4.56 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 = 0.49   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 = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3039
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.1045

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= 0.207
  Angle     :  0.516   7.219   9177  Z= 0.276
  Chirality :  0.042   0.158   1103
  Planarity :  0.003   0.040   1145
  Dihedral  : 10.629 178.694    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  : 0.756 
Fit side-chains
REVERT: A  267 GLN cc_start: 0.8118 (tp-100) cc_final: 0.7659 (tp-100)
REVERT: A  311 TYR cc_start: 0.8357 (m-80) cc_final: 0.8149 (m-80)
  outliers start: 6
  outliers final: 4
  residues processed: 80
  average time/residue: 0.1770
  time to fit residues: 19.4899
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  : 0.717 
-------------------------------------------------------------------------------
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:    0.0970
   chunk 44 optimal weight:    0.9990
   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:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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 = 0.3524 r_free = 0.3524 target = 0.124808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.097091 restraints weight = 43347.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 5.42
r_work: 0.2984 rms_B_bonded: 5.29 restraints_weight: 2.0000
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2986
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2986 r_free = 0.2986    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2986 r_free = 0.2986    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2986
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.1351

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= 0.140
  Angle     :  0.465   7.314   9177  Z= 0.246
  Chirality :  0.040   0.158   1103
  Planarity :  0.003   0.038   1145
  Dihedral  : 10.394 179.721    990
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 10.27 %
    Favored  : 89.04 %
  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:  1.20 (0.29), residues: 889
  helix:  2.31 (0.26), residues: 410
  sheet:  0.09 (0.39), residues: 181
  loop : -0.91 (0.33), residues: 298

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   0.011   0.001   PHE A 212 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.001   0.000   ARG R  63 

*********************** 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
  82 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.753 
Fit side-chains
REVERT: A  267 GLN cc_start: 0.7975 (tp-100) cc_final: 0.7516 (tp-100)
REVERT: B  155 ASN cc_start: 0.7990 (t0) cc_final: 0.7743 (t0)
  outliers start: 4
  outliers final: 3
  residues processed: 81
  average time/residue: 0.1841
  time to fit residues: 20.5024
Evaluate side-chains
  77 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain R residue  143 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:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.9182

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.123595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.095761 restraints weight = 35046.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 4.60
r_work: 0.2998 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2994
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    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 = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2994
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6703  Z= 0.170
  Angle     :  0.473   7.634   9177  Z= 0.248
  Chirality :  0.041   0.168   1103
  Planarity :  0.003   0.037   1145
  Dihedral  : 10.256 178.562    990
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 2.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 11.47 %
    Favored  : 86.99 %
  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:  1.28 (0.29), residues: 889
  helix:  2.38 (0.27), residues: 410
  sheet:  0.15 (0.39), residues: 181
  loop : -0.89 (0.34), residues: 298

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   0.010   0.001   PHE A 212 
 TYR   0.012   0.001   TYR B  59 
 ARG   0.001   0.000   ARG A 389 

*********************** 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
  91 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.681 
Fit side-chains
REVERT: B  259 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8482 (pt0)
  outliers start: 9
  outliers final: 7
  residues processed: 88
  average time/residue: 0.1797
  time to fit residues: 21.4601
Evaluate side-chains
  84 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain G residue   15 LEU
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:    0.1980
   chunk 22 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 35 optimal weight:    0.1980
   chunk 88 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0970
   chunk 13 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.4378

-------------------------------------------------------------------------------
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 = 0.3545 r_free = 0.3545 target = 0.126287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.098389 restraints weight = 32496.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 4.48
r_work: 0.3046 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3038
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3038
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
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      :  0.002   0.019   6703  Z= 0.116
  Angle     :  0.444   7.481   9177  Z= 0.231
  Chirality :  0.039   0.182   1103
  Planarity :  0.003   0.037   1145
  Dihedral  : 10.149 178.976    990
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 13.18 %
    Favored  : 85.62 %
  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:  1.40 (0.29), residues: 889
  helix:  2.55 (0.27), residues: 404
  sheet:  0.25 (0.40), residues: 181
  loop : -0.89 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 277 
 HIS   0.006   0.001   HIS R 241 
 PHE   0.009   0.001   PHE A 212 
 TYR   0.006   0.001   TYR A 339 
 ARG   0.005   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: 7
    poor density    : 79
  time to evaluate  : 0.783 
Fit side-chains
  outliers start: 7
  outliers final: 3
  residues processed: 84
  average time/residue: 0.1736
  time to fit residues: 19.9961
Evaluate side-chains
  75 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain R residue  236 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0060
   chunk 59 optimal weight:    1.9990
   chunk 37 optimal weight:    0.2980
   chunk 85 optimal weight:    7.9990
   chunk 20 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.5596

-------------------------------------------------------------------------------
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 = 0.3538 r_free = 0.3538 target = 0.125683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.098449 restraints weight = 27866.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 4.15
r_work: 0.3040 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.3040
-------------------------------------------------------------------------------
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 = 0.42   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 = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3050
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.1829

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= 0.126
  Angle     :  0.444   7.530   9177  Z= 0.231
  Chirality :  0.040   0.183   1103
  Planarity :  0.003   0.036   1145
  Dihedral  : 10.090 178.804    990
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 13.70 %
    Favored  : 84.76 %
  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:  1.45 (0.29), residues: 889
  helix:  2.59 (0.27), residues: 404
  sheet:  0.25 (0.40), residues: 181
  loop : -0.87 (0.34), residues: 304

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   0.008   0.001   TYR R 219 
 ARG   0.005   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
  87 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.802 
Fit side-chains
REVERT: B  259 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8412 (pt0)
  outliers start: 9
  outliers final: 8
  residues processed: 85
  average time/residue: 0.1765
  time to fit residues: 20.9005
Evaluate side-chains
  81 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
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   25 CYS
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 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:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3517 r_free = 0.3517 target = 0.124071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.096473 restraints weight = 31016.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 4.34
r_work: 0.3009 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3013
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3013 r_free = 0.3013    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3013 r_free = 0.3013    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3013
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.1802

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= 0.168
  Angle     :  0.460   7.598   9177  Z= 0.240
  Chirality :  0.040   0.190   1103
  Planarity :  0.003   0.036   1145
  Dihedral  : 10.094 178.760    990
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.55 %
    Favored  : 83.39 %
  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:  2.50 (0.27), residues: 410
  sheet:  0.15 (0.39), residues: 182
  loop : -0.79 (0.34), residues: 297

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   0.009   0.001   PHE A 212 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.004   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
  88 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.744 
Fit side-chains
REVERT: B  259 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8489 (pt0)
  outliers start: 12
  outliers final: 9
  residues processed: 85
  average time/residue: 0.1751
  time to fit residues: 20.4717
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  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain B residue   25 CYS
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:    0.0870
   chunk 85 optimal weight:    6.9990
   chunk 87 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 84 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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 = 0.125193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.097395 restraints weight = 34147.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 4.55
r_work: 0.3014 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3022
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3022
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1900

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= 0.130
  Angle     :  0.444   7.542   9177  Z= 0.230
  Chirality :  0.040   0.195   1103
  Planarity :  0.003   0.036   1145
  Dihedral  : 10.066 178.982    990
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.73 %
    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:  1.42 (0.29), residues: 889
  helix:  2.58 (0.26), residues: 404
  sheet:  0.20 (0.39), residues: 181
  loop : -0.87 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 241 
 PHE   0.008   0.001   PHE A 212 
 TYR   0.007   0.001   TYR A 339 
 ARG   0.004   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
  88 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.751 
Fit side-chains
REVERT: B  259 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8453 (pt0)
  outliers start: 12
  outliers final: 8
  residues processed: 86
  average time/residue: 0.1739
  time to fit residues: 20.6866
Evaluate side-chains
  84 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain B residue   25 CYS
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:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 26 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    0.3980
   chunk 36 optimal weight:    4.9990
   overall best weight:    1.2582

-------------------------------------------------------------------------------
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 = 0.3523 r_free = 0.3523 target = 0.123500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.097017 restraints weight = 42645.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 5.08
r_work: 0.2995 rms_B_bonded: 5.05 restraints_weight: 2.0000
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3012
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3012
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6703  Z= 0.210
  Angle     :  0.481   8.326   9177  Z= 0.251
  Chirality :  0.041   0.190   1103
  Planarity :  0.003   0.036   1145
  Dihedral  : 10.106 178.450    990
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 14.90 %
    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:  1.40 (0.29), residues: 889
  helix:  2.48 (0.27), residues: 410
  sheet:  0.13 (0.38), residues: 188
  loop : -0.80 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  82 
 HIS   0.007   0.001   HIS R 241 
 PHE   0.010   0.001   PHE R 289 
 TYR   0.009   0.001   TYR A 253 
 ARG   0.003   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
  88 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.726 
Fit side-chains
REVERT: A  207 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8434 (mm)
  outliers start: 11
  outliers final: 9
  residues processed: 86
  average time/residue: 0.1776
  time to fit residues: 21.0760
Evaluate side-chains
  85 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  156 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:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 63 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 64 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9980
   chunk 61 optimal weight:    0.3980
   chunk 14 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0060
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
B 259 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 = 0.3549 r_free = 0.3549 target = 0.125537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.099980 restraints weight = 24758.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 3.78
r_work: 0.3104 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3100
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3100 r_free = 0.3100    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3100 r_free = 0.3100    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3100
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1955

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= 0.137
  Angle     :  0.453   8.427   9177  Z= 0.235
  Chirality :  0.040   0.197   1103
  Planarity :  0.003   0.037   1145
  Dihedral  : 10.067 178.718    990
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 2.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 15.41 %
    Favored  : 83.05 %
  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:  1.43 (0.29), residues: 889
  helix:  2.57 (0.27), residues: 405
  sheet:  0.16 (0.38), residues: 187
  loop : -0.85 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 241 
 PHE   0.008   0.001   PHE A 212 
 TYR   0.008   0.001   TYR A 339 
 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
  89 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.708 
Fit side-chains
REVERT: A  207 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8231 (pt)
REVERT: A  349 SER cc_start: 0.9054 (p) cc_final: 0.8788 (p)
  outliers start: 9
  outliers final: 7
  residues processed: 87
  average time/residue: 0.1756
  time to fit residues: 21.1922
Evaluate side-chains
  86 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   98 SER
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 72 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 5 optimal weight:    7.9990
   chunk 85 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.3487 r_free = 0.3487 target = 0.120553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.095007 restraints weight = 26048.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 3.80
r_work: 0.3024 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3017
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3017
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6703  Z= 0.321
  Angle     :  0.543   8.655   9177  Z= 0.287
  Chirality :  0.043   0.205   1103
  Planarity :  0.003   0.035   1145
  Dihedral  : 10.191 177.858    990
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 15.41 %
    Favored  : 83.05 %
  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:  1.07 (0.29), residues: 889
  helix:  2.15 (0.26), residues: 418
  sheet:  0.05 (0.38), residues: 186
  loop : -1.02 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.007   0.001   HIS R 241 
 PHE   0.018   0.002   PHE R 289 
 TYR   0.012   0.001   TYR A 253 
 ARG   0.002   0.000   ARG B  68 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3542.19 seconds
wall clock time: 63 minutes 36.35 seconds (3816.35 seconds total)