Starting phenix.real_space_refine
on Tue Feb 11 12:43:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uo4_42427/02_2025/8uo4_42427.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uo4_42427/02_2025/8uo4_42427.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uo4_42427/02_2025/8uo4_42427.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uo4_42427/02_2025/8uo4_42427.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uo4_42427/02_2025/8uo4_42427.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uo4_42427/02_2025/8uo4_42427.cif"
  }
  resolution = 4.0
  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=   0.015
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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      16      5.16       5
     C    3576      2.51       5
     N    1034      2.21       5
     O    1072      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5702
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1854
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 1854
          Classifications: {'peptide': 292}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 157}
          Link IDs: {'PTRANS': 7, 'TRANS': 284}
          Chain breaks: 8
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 610
          Unresolved non-hydrogen angles: 758
          Unresolved non-hydrogen dihedrals: 495
          Unresolved non-hydrogen chiralities: 36
          Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 13, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 27, 'ARG:plan': 21}
          Unresolved non-hydrogen planarities: 392
    Chain: "B"
      Number of atoms: 2224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2224
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 364
          Unresolved non-hydrogen angles: 457
          Unresolved non-hydrogen dihedrals: 282
          Unresolved non-hydrogen chiralities: 24
          Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 11, 'ASP:plan': 20, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 12}
          Unresolved non-hydrogen planarities: 241
    Chain: "G"
      Number of atoms: 307
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 307
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 99
          Unresolved non-hydrogen angles: 119
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 48
    Chain: "R"
      Number of atoms: 1269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1269
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 169}
          Link IDs: {'PTRANS': 6, 'TRANS': 223}
          Chain breaks: 7
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 617
          Unresolved non-hydrogen angles: 809
          Unresolved non-hydrogen dihedrals: 514
          Unresolved non-hydrogen chiralities: 81
          Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 5, 'HIS:plan': 4, 'PHE:plan': 15, 'GLU:plan': 5, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 309
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.72, per 1000 atoms: 0.83
  Number of scatterers: 5702
  At special positions: 0
  Unit cell: (85.0346, 137.097, 100.653, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      16     16.00
     P       3     15.00
     Mg      1     11.99
     O    1072      8.00
     N    1034      7.00
     C    3576      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.64
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1732

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 8 sheets defined
      44.8% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 40
      removed outlier: 3.915A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   TYR A  37 " --> pdb=" O   ASP A  33 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ARG A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 65
      removed outlier: 3.813A  pdb=" N   LYS A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLN A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LEU A  63 " --> pdb=" O   GLN A  59 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   HIS A  64 " --> pdb=" O   MET A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 113
      removed outlier: 3.601A  pdb=" N   ASN A  97 " --> pdb=" O   GLN A  93 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ASN A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLU A 101 " --> pdb=" O   ASN A  97 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ILE A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ILE A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL A 107 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   SER A 111 " --> pdb=" O   VAL A 107 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   ASN A 112 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 157
      removed outlier: 3.505A  pdb=" N   ALA A 152 " --> pdb=" O   GLU A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 165
      removed outlier: 3.825A  pdb=" N   GLU A 164 " --> pdb=" O   ARG A 160 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ARG A 165 " --> pdb=" O   ALA A 161 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 160 through 165'
    Processing helix  chain 'A' and resid 266 through 278
      removed outlier: 3.561A  pdb=" N   ASN A 271 " --> pdb=" O   GLN A 267 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   LEU A 272 " --> pdb=" O   GLU A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.866A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.643A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 382
    Processing helix  chain 'A' and resid 383 through 389
      removed outlier: 3.906A  pdb=" N   HIS A 387 " --> pdb=" O   ILE A 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 4.189A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA B  11 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 12 through 24
    Processing helix  chain 'G' and resid 32 through 44
    Processing helix  chain 'R' and resid 36 through 55
      removed outlier: 3.744A  pdb=" N   ILE R  43 " --> pdb=" O   VAL R  39 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ILE R  47 " --> pdb=" O   ILE R  43 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   VAL R  48 " --> pdb=" O   VAL R  44 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   PHE R  49 " --> pdb=" O   LEU R  45 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY R  50 " --> pdb=" O   ALA R  46 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 70 through 91
      removed outlier: 3.853A  pdb=" N   SER R  74 " --> pdb=" O   TYR R  70 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.509A  pdb=" N   CYS R 106 " --> pdb=" O   GLY R 102 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLU R 107 " --> pdb=" O   ASN R 103 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL R 114 " --> pdb=" O   THR R 110 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   LEU R 115 " --> pdb=" O   SER R 111 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ILE R 135 " --> pdb=" O   ARG R 131 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   SER R 137 " --> pdb=" O   PHE R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 147 through 171
      removed outlier: 3.569A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 179 through 184
      removed outlier: 3.927A  pdb=" N   ASN R 183 " --> pdb=" O   GLN R 179 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   CYS R 184 " --> pdb=" O   GLU R 180 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 179 through 184'
    Processing helix  chain 'R' and resid 198 through 208
    Processing helix  chain 'R' and resid 209 through 234
      removed outlier: 4.092A  pdb=" N   VAL R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ILE R 233 " --> pdb=" O   GLN R 229 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   ASP R 234 " --> pdb=" O   LEU R 230 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 296
      removed outlier: 4.040A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.962A  pdb=" N   HIS R 296 " --> pdb=" O   VAL R 292 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 326
      removed outlier: 3.566A  pdb=" N   ILE R 309 " --> pdb=" O   LYS R 305 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   LEU R 310 " --> pdb=" O   GLU R 306 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU R 311 " --> pdb=" O   VAL R 307 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASN R 312 " --> pdb=" O   TYR R 308 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   TYR R 316 " --> pdb=" O   ASN R 312 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 212
      removed outlier: 3.531A  pdb=" N   THR A 210 " --> pdb=" O   MET A 221 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.207A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 104 through 105
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.778A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 178 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.947A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LEU B 210 " --> pdb=" O   GLN B 220 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.493A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.268A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ALA B 287 " --> pdb=" O   ASN B 295 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   TYR B 289 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 5.152A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 318 through 320
      removed outlier: 3.615A  pdb=" N   ALA B 328 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)

    291 hydrogen bonds defined for protein.
    858 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: 1.56

  Time building geometry restraints manager: 1.90 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1959
        1.34 -     1.46: 1163
        1.46 -     1.58: 2638
        1.58 -     1.69: 5
        1.69 -     1.81: 20
  Bond restraints: 5785
  Sorted by residual:
  bond pdb=" N   ILE A 383 "
       pdb=" CA  ILE A 383 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.09e-02 8.42e+03 1.27e+01
  bond pdb=" N   TYR A 391 "
       pdb=" CA  TYR A 391 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.21e-02 6.83e+03 7.00e+00
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.449 -0.052 2.00e-02 2.50e+03 6.75e+00
  bond pdb=" N   MET A 386 "
       pdb=" CA  MET A 386 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.16e+00
  bond pdb=" N   ARG A 380 "
       pdb=" CA  ARG A 380 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.06e+00
  ... (remaining 5780 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.96: 7886
        2.96 -     5.93: 62
        5.93 -     8.89: 11
        8.89 -    11.86: 4
       11.86 -    14.82: 1
  Bond angle restraints: 7964
  Sorted by residual:
  angle pdb=" N   ILE A 383 "
        pdb=" CA  ILE A 383 "
        pdb=" C   ILE A 383 "
      ideal   model   delta    sigma   weight residual
     111.88  102.30    9.58 1.06e+00 8.90e-01 8.17e+01
  angle pdb=" N   ASN A 377 "
        pdb=" CA  ASN A 377 "
        pdb=" C   ASN A 377 "
      ideal   model   delta    sigma   weight residual
     111.71  105.31    6.40 1.15e+00 7.56e-01 3.09e+01
  angle pdb=" PB  GTP A 401 "
        pdb=" O3B GTP A 401 "
        pdb=" PG  GTP A 401 "
      ideal   model   delta    sigma   weight residual
     120.50  135.32  -14.82 3.00e+00 1.11e-01 2.44e+01
  angle pdb=" CA  GLN A 390 "
        pdb=" C   GLN A 390 "
        pdb=" O   GLN A 390 "
      ideal   model   delta    sigma   weight residual
     121.84  116.75    5.09 1.16e+00 7.43e-01 1.92e+01
  angle pdb=" N   GLU A 392 "
        pdb=" CA  GLU A 392 "
        pdb=" C   GLU A 392 "
      ideal   model   delta    sigma   weight residual
     109.96  103.66    6.30 1.49e+00 4.50e-01 1.79e+01
  ... (remaining 7959 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.19: 3274
       29.19 -    58.39: 51
       58.39 -    87.58: 3
       87.58 -   116.77: 1
      116.77 -   145.97: 1
  Dihedral angle restraints: 3330
    sinusoidal: 687
      harmonic: 2643
  Sorted by residual:
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -41.37  145.97     1      2.00e+01 2.50e-03 4.39e+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  150.85  110.02     1      2.00e+01 2.50e-03 3.22e+01
  dihedral pdb=" CA  CYS A 237 "
           pdb=" C   CYS A 237 "
           pdb=" N   PHE A 238 "
           pdb=" CA  PHE A 238 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.73   17.27     0      5.00e+00 4.00e-02 1.19e+01
  ... (remaining 3327 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 883
       0.067 -    0.133: 100
       0.133 -    0.200: 5
       0.200 -    0.266: 3
       0.266 -    0.333: 1
  Chirality restraints: 992
  Sorted by residual:
  chirality pdb=" CA  ILE A 383 "
            pdb=" N   ILE A 383 "
            pdb=" C   ILE A 383 "
            pdb=" CB  ILE A 383 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.77   -0.33 2.00e-01 2.50e+01 2.77e+00
  chirality pdb=" CA  GLU A 392 "
            pdb=" N   GLU A 392 "
            pdb=" C   GLU A 392 "
            pdb=" CB  GLU A 392 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  ILE A 382 "
            pdb=" N   ILE A 382 "
            pdb=" C   ILE A 382 "
            pdb=" CB  ILE A 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 989 not shown)

  Planarity restraints: 1040
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 376 "    0.012 2.00e-02 2.50e+03   2.56e-02 6.57e+00
        pdb=" C   PHE A 376 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   PHE A 376 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ASN A 377 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 382 "    0.007 2.00e-02 2.50e+03   1.49e-02 2.23e+00
        pdb=" C   ILE A 382 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ILE A 382 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ILE A 383 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "    0.025 5.00e-02 4.00e+02   3.73e-02 2.22e+00
        pdb=" N   PRO G  49 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1037 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 2040
        2.84 -     3.35: 5330
        3.35 -     3.87: 8398
        3.87 -     4.38: 8555
        4.38 -     4.90: 14978
  Nonbonded interactions: 39301
  Sorted by model distance:
  nonbonded pdb=" O   SER G  31 "
            pdb=" OG  SER G  31 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.345 3.040
  nonbonded pdb=" OG  SER A  54 "
            pdb=" OD2 ASP A 223 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.371 3.040
  nonbonded pdb=" O   GLY B 141 "
            pdb=" NE2 GLN B 176 "
     model   vdw
     2.374 3.120
  ... (remaining 39296 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.690
  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:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.100
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
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      :  0.004   0.052   5785  Z= 0.276
  Angle     :  0.716  14.824   7964  Z= 0.406
  Chirality :  0.045   0.333    992
  Planarity :  0.003   0.037   1040
  Dihedral  : 11.999 145.967   1598
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  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: -0.04 (0.29), residues: 870
  helix:  1.82 (0.28), residues: 353
  sheet: -1.40 (0.42), residues: 159
  loop : -1.25 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.006   0.002   HIS B  54 
 PHE   0.012   0.001   PHE B 235 
 TYR   0.005   0.001   TYR B 105 
 ARG   0.002   0.000   ARG A 317 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.597 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1336
  time to fit residues: 15.8255
Evaluate side-chains
  58 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 68 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 70 optimal weight:   20.0000
   chunk 27 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.108534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.091401 restraints weight = 16215.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.091076 restraints weight = 13406.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.092242 restraints weight = 11707.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.1504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   5785  Z= 0.195
  Angle     :  0.511   7.206   7964  Z= 0.280
  Chirality :  0.041   0.143    992
  Planarity :  0.003   0.035   1040
  Dihedral  :  7.059 140.165    958
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 10.06 %
    Favored  : 87.20 %
  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: -0.02 (0.29), residues: 870
  helix:  1.62 (0.27), residues: 381
  sheet: -1.19 (0.41), residues: 165
  loop : -1.31 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 339 
 HIS   0.006   0.001   HIS B  54 
 PHE   0.011   0.001   PHE B 292 
 TYR   0.018   0.001   TYR B 124 
 ARG   0.002   0.000   ARG B 314 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.598 
Fit side-chains
REVERT: B  339 TRP cc_start: 0.8632 (OUTLIER) cc_final: 0.8246 (m-10)
REVERT: G   41 CYS cc_start: 0.8145 (m) cc_final: 0.7668 (p)
  outliers start: 9
  outliers final: 8
  residues processed: 63
  average time/residue: 0.0926
  time to fit residues: 9.6478
Evaluate side-chains
  67 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  285 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 68 optimal weight:   20.0000
   chunk 85 optimal weight:    8.9990
   chunk 60 optimal weight:    5.9990
   chunk 66 optimal weight:    0.0170
   chunk 83 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 88 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   chunk 52 optimal weight:    0.4980
   chunk 86 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   overall best weight:    1.2420

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.108473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.091158 restraints weight = 16446.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.090685 restraints weight = 13602.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.091448 restraints weight = 12182.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   5785  Z= 0.187
  Angle     :  0.474   6.602   7964  Z= 0.258
  Chirality :  0.040   0.133    992
  Planarity :  0.003   0.034   1040
  Dihedral  :  6.650 133.415    958
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 10.37 %
    Favored  : 86.28 %
  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:  0.11 (0.29), residues: 870
  helix:  1.81 (0.27), residues: 380
  sheet: -1.17 (0.41), residues: 167
  loop : -1.34 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 234 
 HIS   0.007   0.001   HIS B  54 
 PHE   0.009   0.001   PHE A 315 
 TYR   0.014   0.001   TYR B 124 
 ARG   0.003   0.001   ARG A 232 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.669 
Fit side-chains
REVERT: B  234 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.7824 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 65
  average time/residue: 0.0903
  time to fit residues: 9.6768
Evaluate side-chains
  66 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  127 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 88 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0020
   chunk 0 optimal weight:   20.0000
   chunk 18 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 69 optimal weight:    7.9990
   chunk 29 optimal weight:   30.0000
   chunk 20 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.1592

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.108871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.091484 restraints weight = 16821.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.091032 restraints weight = 13977.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.092077 restraints weight = 12309.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   5785  Z= 0.172
  Angle     :  0.453   6.350   7964  Z= 0.246
  Chirality :  0.040   0.131    992
  Planarity :  0.003   0.033   1040
  Dihedral  :  6.453 129.586    958
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 12.20 %
    Favored  : 84.15 %
  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:  0.22 (0.29), residues: 870
  helix:  1.96 (0.27), residues: 380
  sheet: -1.17 (0.40), residues: 170
  loop : -1.31 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 234 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.009   0.001   PHE B 235 
 TYR   0.010   0.001   TYR B 124 
 ARG   0.002   0.000   ARG B 314 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.715 
Fit side-chains
REVERT: A  234 TRP cc_start: 0.8392 (p90) cc_final: 0.8174 (p-90)
REVERT: B  234 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.7822 (m-80)
REVERT: B  339 TRP cc_start: 0.8587 (m100) cc_final: 0.8074 (m-10)
  outliers start: 12
  outliers final: 8
  residues processed: 64
  average time/residue: 0.0926
  time to fit residues: 9.7283
Evaluate side-chains
  66 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  285 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 59 optimal weight:    9.9990
   chunk 49 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 9 optimal weight:    0.2980
   chunk 62 optimal weight:    5.9990
   chunk 79 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 29 optimal weight:   30.0000
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN

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 = 0.107113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.089703 restraints weight = 16655.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.089273 restraints weight = 13910.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.090403 restraints weight = 12280.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   5785  Z= 0.246
  Angle     :  0.492   6.085   7964  Z= 0.268
  Chirality :  0.041   0.144    992
  Planarity :  0.003   0.037   1040
  Dihedral  :  6.492 127.437    958
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 11.28 %
    Favored  : 83.54 %
  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:  0.14 (0.29), residues: 870
  helix:  1.87 (0.27), residues: 379
  sheet: -1.19 (0.41), residues: 165
  loop : -1.34 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 234 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.013   0.002   PHE B 235 
 TYR   0.013   0.001   TYR A 360 
 ARG   0.002   0.001   ARG B 314 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.667 
Fit side-chains
REVERT: B  234 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.7788 (m-80)
  outliers start: 17
  outliers final: 12
  residues processed: 67
  average time/residue: 0.0931
  time to fit residues: 10.2650
Evaluate side-chains
  69 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue  124 LEU
Chi-restraints excluded: chain R residue  127 ILE
Chi-restraints excluded: chain R residue  285 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   chunk 6 optimal weight:   20.0000
   chunk 60 optimal weight:    0.6980
   chunk 16 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.107930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.090071 restraints weight = 16275.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.089662 restraints weight = 13091.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.090367 restraints weight = 11353.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   5785  Z= 0.188
  Angle     :  0.462   6.030   7964  Z= 0.249
  Chirality :  0.040   0.128    992
  Planarity :  0.003   0.036   1040
  Dihedral  :  6.293 124.103    958
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 14.02 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.29), residues: 870
  helix:  2.00 (0.28), residues: 380
  sheet: -1.26 (0.41), residues: 162
  loop : -1.31 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 297 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.010   0.001   PHE B 235 
 TYR   0.010   0.001   TYR A 360 
 ARG   0.002   0.000   ARG B 314 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.642 
Fit side-chains
REVERT: B  234 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.7667 (m-80)
  outliers start: 13
  outliers final: 11
  residues processed: 66
  average time/residue: 0.0928
  time to fit residues: 10.0589
Evaluate side-chains
  68 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  124 LEU
Chi-restraints excluded: chain R residue  127 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 89 optimal weight:    0.0980
   chunk 73 optimal weight:    0.9980
   chunk 69 optimal weight:    8.9990
   chunk 2 optimal weight:    5.9990
   chunk 17 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 77 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.109147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.091251 restraints weight = 16271.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.091043 restraints weight = 12421.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.091734 restraints weight = 11013.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   5785  Z= 0.146
  Angle     :  0.438   6.046   7964  Z= 0.236
  Chirality :  0.039   0.126    992
  Planarity :  0.003   0.034   1040
  Dihedral  :  5.956 118.105    958
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 14.33 %
    Favored  : 81.40 %
  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:  0.40 (0.29), residues: 870
  helix:  2.19 (0.28), residues: 381
  sheet: -1.24 (0.41), residues: 165
  loop : -1.27 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.002   0.001   HIS B 225 
 PHE   0.009   0.001   PHE A 212 
 TYR   0.008   0.001   TYR B 124 
 ARG   0.002   0.000   ARG B 314 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A  234 TRP cc_start: 0.8501 (p90) cc_final: 0.8171 (p-90)
REVERT: B   61 MET cc_start: 0.9019 (ppp) cc_final: 0.8285 (ppp)
REVERT: B  234 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.7595 (m-80)
  outliers start: 14
  outliers final: 10
  residues processed: 72
  average time/residue: 0.1089
  time to fit residues: 12.1118
Evaluate side-chains
  69 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  124 LEU
Chi-restraints excluded: chain R residue  127 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 42 optimal weight:    8.9990
   chunk 65 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0970
   chunk 80 optimal weight:    0.0040
   chunk 59 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
R 318 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.110046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.092745 restraints weight = 16107.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.092452 restraints weight = 13115.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.093541 restraints weight = 11738.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   5785  Z= 0.126
  Angle     :  0.433   6.081   7964  Z= 0.231
  Chirality :  0.039   0.125    992
  Planarity :  0.003   0.032   1040
  Dihedral  :  5.761 114.109    958
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 16.16 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.30), residues: 870
  helix:  2.33 (0.28), residues: 381
  sheet: -1.20 (0.41), residues: 166
  loop : -1.22 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 297 
 HIS   0.002   0.001   HIS B  54 
 PHE   0.008   0.001   PHE A 212 
 TYR   0.008   0.001   TYR B 124 
 ARG   0.006   0.000   ARG B 304 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.633 
Fit side-chains
REVERT: A  234 TRP cc_start: 0.8436 (p90) cc_final: 0.8105 (p-90)
REVERT: B   61 MET cc_start: 0.9083 (ppp) cc_final: 0.8312 (ppp)
REVERT: B  234 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.7602 (m-80)
REVERT: B  339 TRP cc_start: 0.8568 (m100) cc_final: 0.8001 (m-10)
  outliers start: 12
  outliers final: 9
  residues processed: 70
  average time/residue: 0.1105
  time to fit residues: 11.8394
Evaluate side-chains
  71 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  127 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 21 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0770
   chunk 5 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 60 optimal weight:    0.9990
   chunk 29 optimal weight:   30.0000
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.9742

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.109412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.092176 restraints weight = 16214.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.091924 restraints weight = 13225.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.092975 restraints weight = 11660.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   5785  Z= 0.153
  Angle     :  0.443   5.981   7964  Z= 0.236
  Chirality :  0.039   0.126    992
  Planarity :  0.003   0.033   1040
  Dihedral  :  5.689 111.380    958
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 15.24 %
    Favored  : 80.49 %
  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:  0.57 (0.29), residues: 870
  helix:  2.33 (0.27), residues: 381
  sheet: -1.04 (0.42), residues: 161
  loop : -1.26 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 297 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.010   0.001   PHE B 292 
 TYR   0.008   0.001   TYR B 124 
 ARG   0.003   0.000   ARG B 304 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.640 
Fit side-chains
REVERT: A  234 TRP cc_start: 0.8494 (p90) cc_final: 0.8180 (p-90)
REVERT: B   61 MET cc_start: 0.9081 (ppp) cc_final: 0.8331 (ppp)
REVERT: B  234 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.7565 (m-80)
  outliers start: 14
  outliers final: 11
  residues processed: 68
  average time/residue: 0.1145
  time to fit residues: 12.0593
Evaluate side-chains
  69 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  127 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 20 optimal weight:    0.4980
   chunk 71 optimal weight:    0.0670
   chunk 78 optimal weight:    1.9990
   chunk 55 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0670
   chunk 84 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 6 optimal weight:   20.0000
   chunk 66 optimal weight:    8.9990
   chunk 80 optimal weight:   10.0000
   overall best weight:    0.7260

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.109901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.092465 restraints weight = 16429.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.092119 restraints weight = 13330.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.093185 restraints weight = 11840.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   5785  Z= 0.132
  Angle     :  0.434   5.998   7964  Z= 0.232
  Chirality :  0.039   0.136    992
  Planarity :  0.003   0.032   1040
  Dihedral  :  5.549 108.316    958
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 16.46 %
    Favored  : 79.88 %
  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:  0.72 (0.29), residues: 870
  helix:  2.55 (0.27), residues: 374
  sheet: -0.90 (0.42), residues: 159
  loop : -1.26 (0.31), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 297 
 HIS   0.002   0.001   HIS A 220 
 PHE   0.008   0.001   PHE B 292 
 TYR   0.007   0.001   TYR B 124 
 ARG   0.001   0.000   ARG B 314 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.676 
Fit side-chains
REVERT: A  234 TRP cc_start: 0.8541 (p90) cc_final: 0.8261 (p-90)
REVERT: B   61 MET cc_start: 0.9083 (ppp) cc_final: 0.8333 (ppp)
REVERT: B  234 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.7598 (m-80)
  outliers start: 12
  outliers final: 10
  residues processed: 68
  average time/residue: 0.1123
  time to fit residues: 11.7546
Evaluate side-chains
  68 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASN
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  127 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 87 optimal weight:   20.0000
   chunk 70 optimal weight:   20.0000
   chunk 7 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 29 optimal weight:   30.0000
   chunk 31 optimal weight:   10.0000
   overall best weight:    4.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.108770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.091530 restraints weight = 16170.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.091599 restraints weight = 12114.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.092473 restraints weight = 10974.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.195   5785  Z= 0.436
  Angle     :  0.989  59.148   7964  Z= 0.597
  Chirality :  0.044   0.173    992
  Planarity :  0.003   0.036   1040
  Dihedral  :  5.565 107.839    958
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 17.07 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.12 %
  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:  0.58 (0.29), residues: 870
  helix:  2.40 (0.27), residues: 374
  sheet: -1.00 (0.42), residues: 161
  loop : -1.26 (0.31), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP B  82 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.013   0.002   PHE B 235 
 TYR   0.009   0.001   TYR A 360 
 ARG   0.006   0.001   ARG B 150 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1659.45 seconds
wall clock time: 30 minutes 20.20 seconds (1820.20 seconds total)