Starting phenix.real_space_refine
on Tue Mar 11 21:34:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gfv_29985/03_2025/8gfv_29985.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gfv_29985/03_2025/8gfv_29985.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gfv_29985/03_2025/8gfv_29985.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gfv_29985/03_2025/8gfv_29985.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gfv_29985/03_2025/8gfv_29985.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gfv_29985/03_2025/8gfv_29985.cif"
  }
  resolution = 3.1
  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=   0.033
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      44      5.16       5
     C    4299      2.51       5
     N    1156      2.21       5
     O    1200      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6702
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1771
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 231, 1759
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 165
          Unresolved non-hydrogen angles: 200
          Unresolved non-hydrogen dihedrals: 133
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 119
      Conformer: "B"
        Number of residues, atoms: 231, 1759
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 165
          Unresolved non-hydrogen angles: 200
          Unresolved non-hydrogen dihedrals: 133
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 119
          bond proxies already assigned to first conformer: 1779
    Chain: "B"
      Number of atoms: 2405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2405
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 5, 'TRANS': 323}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 122
          Unresolved non-hydrogen angles: 148
          Unresolved non-hydrogen dihedrals: 96
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 97
    Chain: "G"
      Number of atoms: 332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 332
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 32
    Chain: "R"
      Number of atoms: 2144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2144
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 94
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 72
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "R"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          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: 6.08, per 1000 atoms: 0.91
  Number of scatterers: 6702
  At special positions: 0
  Unit cell: (82.4315, 133.626, 99.7855, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      44     16.00
     P       3     15.00
     O    1200      8.00
     N    1156      7.00
     C    4299      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " 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: 1.73
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1690

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 8 sheets defined
      48.5% alpha, 17.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 40
      removed outlier: 3.801A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.817A  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: 3.852A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.733A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.287A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 3.596A  pdb=" N   ARG A 317 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.572A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.604A  pdb=" N   PHE A 376 " --> pdb=" O   ILE A 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 25
      removed outlier: 3.606A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 13 through 22
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.507A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'R' and resid 36 through 61
      removed outlier: 3.624A  pdb=" N   GLY R  50 " --> pdb=" O   ALA R  46 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 66
      removed outlier: 5.362A  pdb=" N   THR R  66 " --> pdb=" O   ARG R  63 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 97
      removed outlier: 4.123A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.727A  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: 3.891A  pdb=" N   ILE R 121 " --> pdb=" O   VAL R 117 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   GLU R 122 " --> pdb=" O   THR R 118 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 166
      removed outlier: 3.793A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 171
      removed outlier: 3.592A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 175
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.751A  pdb=" N   SER R 204 " --> pdb=" O   ALA R 200 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 238
      removed outlier: 3.742A  pdb=" N   VAL R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   MET R 215 " --> pdb=" O   PRO R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 287
      removed outlier: 3.731A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 288 through 299
      removed outlier: 4.704A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.607A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 318 through 320
      No H-bonds generated for 'chain 'R' and resid 318 through 320'
    Processing helix  chain 'R' and resid 321 through 327
    Processing helix  chain 'R' and resid 329 through 339
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213
      removed outlier: 7.136A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.183A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.171A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.459A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   VAL A 287 " --> pdb=" O  ATYR A 360 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.681A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.857A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.610A  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: 3.569A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.236A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.660A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.888A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.317A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.782A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.745A  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: 3.728A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)

    350 hydrogen bonds defined for protein.
    1011 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.34

  Time building geometry restraints manager: 2.06 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: 2117
        1.34 -     1.46: 1109
        1.46 -     1.57: 3553
        1.57 -     1.69: 5
        1.69 -     1.81: 61
  Bond restraints: 6845
  Sorted by residual:
  bond pdb=" C5  GTP A 401 "
       pdb=" C6  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.476 -0.086 2.00e-02 2.50e+03 1.83e+01
  bond pdb=" C4  GTP A 401 "
       pdb=" C5  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.460 -0.070 2.00e-02 2.50e+03 1.22e+01
  bond pdb=" C4  GTP A 401 "
       pdb=" N9  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.375  1.324  0.051 2.00e-02 2.50e+03 6.61e+00
  bond pdb=" CA  SER A  51 "
       pdb=" C   SER A  51 "
    ideal  model  delta    sigma   weight residual
    1.523  1.491  0.032 1.30e-02 5.92e+03 6.13e+00
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.446 -0.049 2.00e-02 2.50e+03 6.01e+00
  ... (remaining 6840 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 9247
        2.19 -     4.39: 75
        4.39 -     6.58: 17
        6.58 -     8.77: 3
        8.77 -    10.97: 2
  Bond angle restraints: 9344
  Sorted by residual:
  angle pdb=" N   GLY A  49 "
        pdb=" CA  GLY A  49 "
        pdb=" C   GLY A  49 "
      ideal   model   delta    sigma   weight residual
     111.54  118.36   -6.82 1.36e+00 5.41e-01 2.51e+01
  angle pdb=" O1B GTP A 401 "
        pdb=" PB  GTP A 401 "
        pdb=" O2B GTP A 401 "
      ideal   model   delta    sigma   weight residual
     109.50  120.47  -10.97 3.00e+00 1.11e-01 1.34e+01
  angle pdb=" O1A GTP A 401 "
        pdb=" PA  GTP A 401 "
        pdb=" O2A GTP A 401 "
      ideal   model   delta    sigma   weight residual
     109.50  119.81  -10.31 3.00e+00 1.11e-01 1.18e+01
  angle pdb=" N   GLY A  52 "
        pdb=" CA  GLY A  52 "
        pdb=" C   GLY A  52 "
      ideal   model   delta    sigma   weight residual
     113.18  106.37    6.81 2.37e+00 1.78e-01 8.26e+00
  angle pdb=" CA  GLY A  49 "
        pdb=" C   GLY A  49 "
        pdb=" O   GLY A  49 "
      ideal   model   delta    sigma   weight residual
     121.58  119.25    2.33 9.00e-01 1.23e+00 6.68e+00
  ... (remaining 9339 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.41: 3893
       32.41 -    64.82: 79
       64.82 -    97.23: 5
       97.23 -   129.64: 0
      129.64 -   162.05: 3
  Dihedral angle restraints: 3980
    sinusoidal: 1375
      harmonic: 2605
  Sorted by residual:
  dihedral pdb=" CB  CYS R 184 "
           pdb=" SG  CYS R 184 "
           pdb=" SG  CYS R 190 "
           pdb=" CB  CYS R 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  152.46  -59.46     1      1.00e+01 1.00e-02 4.72e+01
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -57.46  162.05     1      2.00e+01 2.50e-03 4.68e+01
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27  -92.40  161.67     1      2.00e+01 2.50e-03 4.68e+01
  ... (remaining 3977 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 656
       0.029 -    0.057: 276
       0.057 -    0.086: 109
       0.086 -    0.115: 53
       0.115 -    0.144: 11
  Chirality restraints: 1105
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.54   -0.14 2.00e-01 2.50e+01 5.16e-01
  chirality pdb=" CA  ILE A 207 "
            pdb=" N   ILE A 207 "
            pdb=" C   ILE A 207 "
            pdb=" CB  ILE A 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.58e-01
  chirality pdb=" CA  ILE A 244 "
            pdb=" N   ILE A 244 "
            pdb=" C   ILE A 244 "
            pdb=" CB  ILE A 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 1102 not shown)

  Planarity restraints: 1167
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "    0.022 5.00e-02 4.00e+02   3.34e-02 1.78e+00
        pdb=" N   PRO G  49 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 210 "    0.022 5.00e-02 4.00e+02   3.33e-02 1.78e+00
        pdb=" N   PRO R 211 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO R 211 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO R 211 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "    0.019 5.00e-02 4.00e+02   2.89e-02 1.34e+00
        pdb=" N   PRO B 194 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1164 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1753
        2.80 -     3.33: 5976
        3.33 -     3.85: 10440
        3.85 -     4.38: 11659
        4.38 -     4.90: 21766
  Nonbonded interactions: 51594
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 343 "
            pdb=" NH2 ARG R 239 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" O   SER R 111 "
            pdb=" OG  SER R 165 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" OH  TYR R 209 "
            pdb=" O   PHE R 290 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.347 3.040
  nonbonded pdb=" OH  TYR R 219 "
            pdb=" O   HOH R 601 "
     model   vdw
     2.397 3.040
  ... (remaining 51589 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:             1.420
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     22.250
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
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   0.086   6845  Z= 0.282
  Angle     :  0.578  10.967   9344  Z= 0.297
  Chirality :  0.041   0.144   1105
  Planarity :  0.003   0.033   1167
  Dihedral  : 14.483 162.053   2284
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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: 879
  helix:  2.01 (0.27), residues: 389
  sheet:  0.79 (0.41), residues: 169
  loop : -0.71 (0.32), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 109 
 HIS   0.011   0.002   HIS B 183 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.005   0.000   ARG A  38 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.751 
Fit side-chains
REVERT: R  113 ASP cc_start: 0.8709 (t70) cc_final: 0.8436 (t0)
REVERT: R  231 GLN cc_start: 0.8333 (tm-30) cc_final: 0.7971 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.2144
  time to fit residues: 28.6354
Evaluate side-chains
  88 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.0050
   chunk 66 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.1598

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
A 236 GLN
B  75 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.121818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.094932 restraints weight = 26008.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 3.53
r_work: 0.2874 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2858
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2858 r_free = 0.2858    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2858
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.0828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6845  Z= 0.214
  Angle     :  0.503   6.505   9344  Z= 0.271
  Chirality :  0.041   0.132   1105
  Planarity :  0.003   0.034   1167
  Dihedral  :  9.701 175.300    985
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 1.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  6.04 %
    Favored  : 93.34 %
  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:  1.38 (0.29), residues: 879
  helix:  2.13 (0.27), residues: 392
  sheet:  0.81 (0.41), residues: 177
  loop : -0.58 (0.33), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 297 
 HIS   0.008   0.002   HIS B 183 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.003   0.000   ARG A  38 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.681 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7576 (mt-10)
REVERT: A   38 ARG cc_start: 0.8588 (mmm-85) cc_final: 0.8195 (mtm110)
REVERT: R  231 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8326 (tm-30)
  outliers start: 4
  outliers final: 4
  residues processed: 95
  average time/residue: 0.2175
  time to fit residues: 26.9127
Evaluate side-chains
  89 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0870
   chunk 0 optimal weight:   20.0000
   chunk 80 optimal weight:    0.0470
   chunk 54 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   overall best weight:    0.7658

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.122940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.096187 restraints weight = 28332.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 3.56
r_work: 0.2894 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2893
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2893 r_free = 0.2893    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2893 r_free = 0.2893    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2893
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.1106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6845  Z= 0.156
  Angle     :  0.458   6.322   9344  Z= 0.246
  Chirality :  0.040   0.131   1105
  Planarity :  0.003   0.033   1167
  Dihedral  :  8.283 156.797    985
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 1.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  8.20 %
    Favored  : 90.87 %
  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:  1.54 (0.29), residues: 879
  helix:  2.28 (0.27), residues: 392
  sheet:  0.87 (0.41), residues: 175
  loop : -0.53 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 297 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.007   0.001   TYR A  37 
 ARG   0.006   0.000   ARG R 239 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.696 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8594 (mmm-85) cc_final: 0.8171 (mtm-85)
REVERT: R  231 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8355 (tm-30)
  outliers start: 6
  outliers final: 6
  residues processed: 94
  average time/residue: 0.2178
  time to fit residues: 26.4035
Evaluate side-chains
  93 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0010
   chunk 52 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.8990

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
A 220 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.122035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.095360 restraints weight = 28136.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3032 rms_B_bonded: 3.45
r_work: 0.2884 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2842
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2842 r_free = 0.2842    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2842 r_free = 0.2842    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2842
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.1186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6845  Z= 0.173
  Angle     :  0.462   6.705   9344  Z= 0.248
  Chirality :  0.041   0.132   1105
  Planarity :  0.003   0.038   1167
  Dihedral  :  8.035 153.343    985
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 1.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  9.29 %
    Favored  : 89.32 %
  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:  1.54 (0.29), residues: 879
  helix:  2.28 (0.27), residues: 393
  sheet:  0.78 (0.40), residues: 175
  loop : -0.47 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 297 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.008   0.001   TYR A  37 
 ARG   0.008   0.000   ARG A 283 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.681 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8606 (mmm-85) cc_final: 0.8204 (mtm-85)
REVERT: B  234 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8052 (t80)
REVERT: R  231 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8368 (tm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 98
  average time/residue: 0.2078
  time to fit residues: 26.4693
Evaluate side-chains
  96 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   chunk 27 optimal weight:    0.5980
   chunk 4 optimal weight:    4.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.119759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.092710 restraints weight = 27146.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 3.59
r_work: 0.2857 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2766
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2766 r_free = 0.2766    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2766 r_free = 0.2766    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2766
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.1206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6845  Z= 0.259
  Angle     :  0.508   7.986   9344  Z= 0.271
  Chirality :  0.042   0.138   1105
  Planarity :  0.003   0.039   1167
  Dihedral  :  8.064 151.280    985
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 1.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 10.22 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.29), residues: 879
  helix:  2.20 (0.27), residues: 393
  sheet:  0.72 (0.39), residues: 175
  loop : -0.52 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 297 
 HIS   0.009   0.002   HIS A 220 
 PHE   0.017   0.002   PHE A 212 
 TYR   0.009   0.001   TYR A 339 
 ARG   0.006   0.000   ARG A 283 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.707 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8704 (mmm-85) cc_final: 0.8220 (mtm-85)
REVERT: B  234 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8216 (t80)
REVERT: R  231 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8339 (tm-30)
  outliers start: 11
  outliers final: 9
  residues processed: 92
  average time/residue: 0.2282
  time to fit residues: 27.4954
Evaluate side-chains
  92 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.121513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.094904 restraints weight = 27980.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 3.54
r_work: 0.2880 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2825
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2825 r_free = 0.2825    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2825 r_free = 0.2825    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2825
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.1321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6845  Z= 0.170
  Angle     :  0.462   7.047   9344  Z= 0.248
  Chirality :  0.041   0.131   1105
  Planarity :  0.003   0.039   1167
  Dihedral  :  7.930 149.609    985
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 10.84 %
    Favored  : 87.46 %
  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:  1.47 (0.29), residues: 879
  helix:  2.27 (0.27), residues: 393
  sheet:  0.70 (0.39), residues: 175
  loop : -0.55 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 297 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.017   0.001   PHE A 212 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.006   0.000   ARG A 283 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8675 (mmm-85) cc_final: 0.8290 (mtm-85)
REVERT: B  234 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8162 (t80)
REVERT: R  231 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8303 (tm-30)
  outliers start: 11
  outliers final: 9
  residues processed: 90
  average time/residue: 0.2145
  time to fit residues: 25.1365
Evaluate side-chains
  89 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0980
   chunk 58 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 85 optimal weight:    0.0970
   chunk 82 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.123618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.098051 restraints weight = 23781.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 3.20
r_work: 0.2947 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2930 r_free = 0.2930    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.1432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6845  Z= 0.130
  Angle     :  0.440   7.051   9344  Z= 0.235
  Chirality :  0.040   0.131   1105
  Planarity :  0.003   0.036   1167
  Dihedral  :  7.767 147.535    985
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 1.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 10.84 %
    Favored  : 87.62 %
  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:  1.58 (0.29), residues: 879
  helix:  2.34 (0.27), residues: 394
  sheet:  0.76 (0.40), residues: 175
  loop : -0.47 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 297 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.017   0.001   PHE A 212 
 TYR   0.009   0.001   TYR R 219 
 ARG   0.007   0.000   ARG R 239 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.773 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8655 (mmm-85) cc_final: 0.8247 (mtm-85)
REVERT: R  231 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8305 (tm-30)
  outliers start: 10
  outliers final: 9
  residues processed: 92
  average time/residue: 0.2283
  time to fit residues: 27.2805
Evaluate side-chains
  94 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain R residue   41 SER
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    0.5980
   chunk 36 optimal weight:    0.3980
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.122893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.097442 restraints weight = 27888.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 3.27
r_work: 0.2910 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2893
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2893 r_free = 0.2893    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2893 r_free = 0.2893    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2893
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6845  Z= 0.147
  Angle     :  0.445   7.138   9344  Z= 0.239
  Chirality :  0.040   0.132   1105
  Planarity :  0.003   0.039   1167
  Dihedral  :  7.729 146.510    985
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 1.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 11.30 %
    Favored  : 87.15 %
  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:  1.61 (0.29), residues: 879
  helix:  2.39 (0.27), residues: 392
  sheet:  0.78 (0.40), residues: 175
  loop : -0.48 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 297 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.008   0.000   ARG A 283 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7557 (mt-10)
REVERT: A   38 ARG cc_start: 0.8708 (mmm-85) cc_final: 0.8303 (mtm-85)
REVERT: B  234 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8136 (t80)
REVERT: R  231 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8387 (tm-30)
  outliers start: 10
  outliers final: 9
  residues processed: 93
  average time/residue: 0.2132
  time to fit residues: 26.0442
Evaluate side-chains
  96 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain R residue   41 SER
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.121015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.095613 restraints weight = 35681.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 3.73
r_work: 0.2874 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2876
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2876 r_free = 0.2876    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2876
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.1374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6845  Z= 0.200
  Angle     :  0.474   7.180   9344  Z= 0.254
  Chirality :  0.041   0.135   1105
  Planarity :  0.003   0.044   1167
  Dihedral  :  7.809 146.190    985
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 1.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.46 %
    Favored  : 86.69 %
  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:  1.54 (0.29), residues: 879
  helix:  2.30 (0.27), residues: 393
  sheet:  0.76 (0.40), residues: 175
  loop : -0.48 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 297 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.017   0.001   PHE A 212 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.007   0.000   ARG R 239 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.769 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.8288 (mtm-85)
REVERT: B  234 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8195 (t80)
REVERT: R  231 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8384 (tm-30)
  outliers start: 12
  outliers final: 10
  residues processed: 91
  average time/residue: 0.2164
  time to fit residues: 25.8950
Evaluate side-chains
  95 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain R residue   41 SER
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 49 optimal weight:    0.2980
   chunk 15 optimal weight:    0.9990
   chunk 37 optimal weight:    0.2980
   chunk 82 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.123601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.098023 restraints weight = 32312.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 3.62
r_work: 0.2921 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2904
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2904 r_free = 0.2904    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2904 r_free = 0.2904    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2904
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6845  Z= 0.133
  Angle     :  0.445   7.129   9344  Z= 0.238
  Chirality :  0.040   0.131   1105
  Planarity :  0.003   0.039   1167
  Dihedral  :  7.709 144.761    985
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 1.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 11.92 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.29), residues: 879
  helix:  2.37 (0.27), residues: 393
  sheet:  0.70 (0.40), residues: 175
  loop : -0.41 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.017   0.001   PHE A 212 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.009   0.000   ARG R 239 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.675 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7555 (mt-10)
REVERT: A   38 ARG cc_start: 0.8683 (mmm-85) cc_final: 0.8244 (mtm-85)
REVERT: B  234 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8019 (t80)
REVERT: R  231 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8349 (tm-30)
  outliers start: 10
  outliers final: 9
  residues processed: 93
  average time/residue: 0.2199
  time to fit residues: 26.6258
Evaluate side-chains
  96 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain R residue   41 SER
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 4 optimal weight:    6.9990
   chunk 71 optimal weight:    0.2980
   chunk 12 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.121658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.096190 restraints weight = 29060.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 3.23
r_work: 0.2902 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2856
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2856
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6845  Z= 0.191
  Angle     :  0.474   7.188   9344  Z= 0.254
  Chirality :  0.041   0.134   1105
  Planarity :  0.003   0.040   1167
  Dihedral  :  7.758 144.887    985
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 1.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.76 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.29), residues: 879
  helix:  2.31 (0.27), residues: 393
  sheet:  0.73 (0.40), residues: 175
  loop : -0.44 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.017   0.001   PHE A 212 
 TYR   0.008   0.001   TYR A  37 
 ARG   0.009   0.000   ARG R 239 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3801.75 seconds
wall clock time: 65 minutes 52.65 seconds (3952.65 seconds total)