Starting phenix.real_space_refine
on Thu Jul 24 21:28:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8unw_42419/07_2025/8unw_42419.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8unw_42419/07_2025/8unw_42419.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8unw_42419/07_2025/8unw_42419.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8unw_42419/07_2025/8unw_42419.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8unw_42419/07_2025/8unw_42419.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8unw_42419/07_2025/8unw_42419.cif"
  }
  resolution = 3.4
  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=   0.023
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      41      5.16       5
     C    4277      2.51       5
     N    1146      2.21       5
     O    1180      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.12s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6647
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1711
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 231, 1699
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 60}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 3
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 226
          Unresolved non-hydrogen angles: 273
          Unresolved non-hydrogen dihedrals: 181
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 14, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 10}
          Unresolved non-hydrogen planarities: 146
      Conformer: "B"
        Number of residues, atoms: 231, 1699
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 60}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 3
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 226
          Unresolved non-hydrogen angles: 273
          Unresolved non-hydrogen dihedrals: 181
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 14, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 10}
          Unresolved non-hydrogen planarities: 146
          bond proxies already assigned to first conformer: 1718
    Chain: "B"
      Number of atoms: 2403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2403
          Classifications: {'peptide': 333}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 46}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 157
          Unresolved non-hydrogen angles: 194
          Unresolved non-hydrogen dihedrals: 120
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 13}
          Unresolved non-hydrogen planarities: 122
    Chain: "G"
      Number of atoms: 352
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 352
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 87
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 36
    Chain: "R"
      Number of atoms: 2133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2133
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 128
          Unresolved non-hydrogen angles: 156
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 83
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR A 360 " occ=0.51
      ... (22 atoms not shown)
      pdb=" OH BTYR A 360 " occ=0.49
  Time building chain proxies: 11.57, per 1000 atoms: 1.74
  Number of scatterers: 6647
  At special positions: 0
  Unit cell: (82.4315, 131.89, 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      41     16.00
     P       3     15.00
     O    1180      8.00
     N    1146      7.00
     C    4277      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: 2.61
  Conformation dependent library (CDL) restraints added in 2.8 seconds
  

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1708

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 8 sheets defined
      48.2% alpha, 15.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 40
      removed outlier: 3.886A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   THR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
      removed outlier: 3.520A  pdb=" N   VAL A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 239
      removed outlier: 3.660A  pdb=" N   ILE A 235 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.555A  pdb=" N   GLU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 3.928A  pdb=" N   ARG A 283 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 302
    Processing helix  chain 'A' and resid 308 through 316
      Proline residue:  A 313  - end of helix
    Processing helix  chain 'A' and resid 333 through 353
      removed outlier: 3.637A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 6 through 25
      removed outlier: 3.740A  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 9 through 24
      removed outlier: 3.909A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.619A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 36 through 61
      removed outlier: 3.580A  pdb=" N   GLY R  50 " --> pdb=" O   ALA R  46 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 65
      removed outlier: 3.514A  pdb=" N   GLN R  65 " --> pdb=" O   GLU R  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 62 through 65'
    Processing helix  chain 'R' and resid 68 through 97
      removed outlier: 3.911A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.564A  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: 3.935A  pdb=" N   ILE R 121 " --> pdb=" O   VAL R 117 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLU R 122 " --> pdb=" O   THR R 118 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 4.568A  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 164
      removed outlier: 3.808A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 165 through 171
      removed outlier: 3.637A  pdb=" N   ILE R 169 " --> pdb=" O   SER R 165 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.557A  pdb=" N   SER R 204 " --> pdb=" O   ALA R 200 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 238
      removed outlier: 3.706A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   MET R 215 " --> pdb=" O   PRO R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 287
      removed outlier: 4.048A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 288 through 299
      removed outlier: 4.695A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.535A  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
      removed outlier: 3.556A  pdb=" N   CYS R 327 " --> pdb=" O   PRO R 323 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 329 through 339
      removed outlier: 3.665A  pdb=" N   LEU R 339 " --> pdb=" O   ALA R 335 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 7.202A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.144A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.039A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.738A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.649A  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: 3.945A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.761A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.326A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.262A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.406A  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: 7.080A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.818A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.795A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.735A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)

    358 hydrogen bonds defined for protein.
    1029 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: 2.41

  Time building geometry restraints manager: 2.50 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1598
        1.33 -     1.45: 1418
        1.45 -     1.57: 3714
        1.57 -     1.69: 5
        1.69 -     1.81: 56
  Bond restraints: 6791
  Sorted by residual:
  bond pdb=" C   ARG A 231 "
       pdb=" N   ARG A 232 "
    ideal  model  delta    sigma   weight residual
    1.331  1.393 -0.063 1.66e-02 3.63e+03 1.43e+01
  bond pdb=" C   ARG A 232 "
       pdb=" N   LYS A 233 "
    ideal  model  delta    sigma   weight residual
    1.334  1.387 -0.053 1.49e-02 4.50e+03 1.25e+01
  bond pdb=" N   GLU A 330 "
       pdb=" CA  GLU A 330 "
    ideal  model  delta    sigma   weight residual
    1.455  1.494 -0.039 1.21e-02 6.83e+03 1.02e+01
  bond pdb=" N   VAL A 301 "
       pdb=" CA  VAL A 301 "
    ideal  model  delta    sigma   weight residual
    1.461  1.497 -0.036 1.19e-02 7.06e+03 9.40e+00
  bond pdb=" N   ILE B  18 "
       pdb=" CA  ILE B  18 "
    ideal  model  delta    sigma   weight residual
    1.461  1.497 -0.036 1.19e-02 7.06e+03 9.36e+00
  ... (remaining 6786 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 8926
        2.34 -     4.68: 307
        4.68 -     7.03: 37
        7.03 -     9.37: 10
        9.37 -    11.71: 3
  Bond angle restraints: 9283
  Sorted by residual:
  angle pdb=" N   LEU G  19 "
        pdb=" CA  LEU G  19 "
        pdb=" C   LEU G  19 "
      ideal   model   delta    sigma   weight residual
     111.71  103.18    8.53 1.15e+00 7.56e-01 5.50e+01
  angle pdb=" N   LEU G  15 "
        pdb=" CA  LEU G  15 "
        pdb=" C   LEU G  15 "
      ideal   model   delta    sigma   weight residual
     111.28  104.28    7.00 1.09e+00 8.42e-01 4.12e+01
  angle pdb=" N   TYR A 253 "
        pdb=" CA  TYR A 253 "
        pdb=" C   TYR A 253 "
      ideal   model   delta    sigma   weight residual
     113.72  105.47    8.25 1.30e+00 5.92e-01 4.03e+01
  angle pdb=" N   ASN A 264 "
        pdb=" CA  ASN A 264 "
        pdb=" C   ASN A 264 "
      ideal   model   delta    sigma   weight residual
     110.35  101.86    8.49 1.36e+00 5.41e-01 3.90e+01
  angle pdb=" CA  PHE A 212 "
        pdb=" CB  PHE A 212 "
        pdb=" CG  PHE A 212 "
      ideal   model   delta    sigma   weight residual
     113.80  119.12   -5.32 1.00e+00 1.00e+00 2.83e+01
  ... (remaining 9278 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.25: 3867
       35.25 -    70.51: 55
       70.51 -   105.76: 1
      105.76 -   141.02: 0
      141.02 -   176.27: 5
  Dihedral angle restraints: 3928
    sinusoidal: 1298
      harmonic: 2630
  Sorted by residual:
  dihedral pdb=" O3A GTP A 401 "
           pdb=" O3B GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PG  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     303.79  127.52  176.27     1      2.00e+01 2.50e-03 4.79e+01
  dihedral pdb=" O2G GTP A 401 "
           pdb=" O3B GTP A 401 "
           pdb=" PG  GTP A 401 "
           pdb=" PB  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.30   15.15  162.15     1      2.00e+01 2.50e-03 4.68e+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  -57.10  161.70     1      2.00e+01 2.50e-03 4.68e+01
  ... (remaining 3925 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 851
       0.056 -    0.111: 190
       0.111 -    0.166: 45
       0.166 -    0.222: 19
       0.222 -    0.277: 4
  Chirality restraints: 1109
  Sorted by residual:
  chirality pdb=" CA  LEU G  15 "
            pdb=" N   LEU G  15 "
            pdb=" C   LEU G  15 "
            pdb=" CB  LEU G  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CA  ILE A 308 "
            pdb=" N   ILE A 308 "
            pdb=" C   ILE A 308 "
            pdb=" CB  ILE A 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  ARG A 231 "
            pdb=" N   ARG A 231 "
            pdb=" C   ARG A 231 "
            pdb=" CB  ARG A 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 1106 not shown)

  Planarity restraints: 1157
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 348 "   -0.015 2.00e-02 2.50e+03   2.97e-02 8.81e+00
        pdb=" C   ILE A 348 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ILE A 348 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   SER A 349 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 212 "    0.011 2.00e-02 2.50e+03   2.36e-02 5.57e+00
        pdb=" C   ASP B 212 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   ASP B 212 "    0.015 2.00e-02 2.50e+03
        pdb=" N   VAL B 213 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN G  18 "   -0.011 2.00e-02 2.50e+03   2.26e-02 5.11e+00
        pdb=" C   GLN G  18 "    0.039 2.00e-02 2.50e+03
        pdb=" O   GLN G  18 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU G  19 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1154 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 797
        2.75 -     3.29: 6336
        3.29 -     3.83: 10423
        3.83 -     4.36: 11413
        4.36 -     4.90: 21090
  Nonbonded interactions: 50059
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 264 "
            pdb=" OD1 ASN A 264 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OH  TYR R 326 "
            pdb=" O   HOH R 601 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OH  TYR R 219 "
            pdb=" O   HOH R 601 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   THR A  55 "
            pdb=" N   LYS A  58 "
     model   vdw
     2.344 3.120
  nonbonded pdb=" OD1 ASP B 205 "
            pdb=" OG  SER B 207 "
     model   vdw
     2.349 3.040
  ... (remaining 50054 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:             2.560
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     34.880
  Find NCS groups from input model:        0.100
  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:5.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
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      :  0.005   0.063   6793  Z= 0.372
  Angle     :  0.917  11.708   9287  Z= 0.622
  Chirality :  0.056   0.277   1109
  Planarity :  0.004   0.059   1157
  Dihedral  : 15.253 176.272   2214
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.78 %
    Favored  : 98.06 %
  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:  0.86 (0.29), residues: 885
  helix:  2.13 (0.28), residues: 378
  sheet: -0.07 (0.40), residues: 179
  loop : -0.90 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 173 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.022   0.001   PHE A 212 
 TYR   0.017   0.001   TYR R 308 
 ARG   0.005   0.000   ARG R 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19308 (  358)
  hydrogen bonds       : angle       6.61005 ( 1029)
  SS BOND              : bond        0.00224 (    2)
  SS BOND              : angle       0.70978 (    4)
  covalent geometry    : bond        0.00548 ( 6791)
  covalent geometry    : angle       0.91673 ( 9283)

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

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.925 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 116
  average time/residue: 0.2879
  time to fit residues: 44.2193
Evaluate side-chains
  91 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 26 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B 119 ASN
B 239 ASN
R 196 ASN
R 312 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.125726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.097093 restraints weight = 33020.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 4.73
r_work: 0.3004 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3015
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3015 r_free = 0.3015    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3015
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6793  Z= 0.161
  Angle     :  0.529   6.955   9287  Z= 0.287
  Chirality :  0.042   0.148   1109
  Planarity :  0.003   0.041   1157
  Dihedral  : 11.599 163.868    989
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  8.91 %
    Favored  : 89.14 %
  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:  0.96 (0.29), residues: 885
  helix:  2.16 (0.27), residues: 387
  sheet: -0.05 (0.41), residues: 176
  loop : -0.85 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.013   0.001   PHE B 241 
 TYR   0.012   0.001   TYR R 316 
 ARG   0.003   0.000   ARG R 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04819 (  358)
  hydrogen bonds       : angle       4.61470 ( 1029)
  SS BOND              : bond        0.00535 (    2)
  SS BOND              : angle       0.88352 (    4)
  covalent geometry    : bond        0.00367 ( 6791)
  covalent geometry    : angle       0.52830 ( 9283)

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

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.981 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.8906 (m-10) cc_final: 0.8507 (m-10)
REVERT: R   82 MET cc_start: 0.7686 (ttt) cc_final: 0.7416 (ttt)
  outliers start: 12
  outliers final: 10
  residues processed: 107
  average time/residue: 0.3148
  time to fit residues: 48.0144
Evaluate side-chains
  97 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 2.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  227 LYS
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  294 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 47 optimal weight:    4.9990
   chunk 58 optimal weight:    0.7980
   chunk 85 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 16 optimal weight:   20.0000
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
R 196 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.123012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.094394 restraints weight = 37562.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 5.38
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3141
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3141
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   6793  Z= 0.182
  Angle     :  0.537   8.807   9287  Z= 0.289
  Chirality :  0.042   0.144   1109
  Planarity :  0.003   0.042   1157
  Dihedral  : 11.314 160.458    989
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 12.80 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.29), residues: 885
  helix:  2.14 (0.27), residues: 386
  sheet: -0.20 (0.40), residues: 176
  loop : -0.90 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.016   0.001   PHE B 241 
 TYR   0.016   0.001   TYR B 111 
 ARG   0.003   0.000   ARG R 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04938 (  358)
  hydrogen bonds       : angle       4.46165 ( 1029)
  SS BOND              : bond        0.00583 (    2)
  SS BOND              : angle       0.88207 (    4)
  covalent geometry    : bond        0.00434 ( 6791)
  covalent geometry    : angle       0.53664 ( 9283)

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

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 1.191 
Fit side-chains
REVERT: R   82 MET cc_start: 0.7772 (ttt) cc_final: 0.7486 (ttp)
  outliers start: 15
  outliers final: 14
  residues processed: 103
  average time/residue: 0.2106
  time to fit residues: 30.0074
Evaluate side-chains
  102 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  227 LYS
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  294 ILE
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 80 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0270
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.7438

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

Flipped N/Q/H residues before XYZ refinement:
R 178 HIS
R 196 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.125281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.096703 restraints weight = 39809.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 5.54
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3177
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3177
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6793  Z= 0.110
  Angle     :  0.479   7.939   9287  Z= 0.256
  Chirality :  0.040   0.147   1109
  Planarity :  0.003   0.039   1157
  Dihedral  : 10.843 163.060    989
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 14.75 %
    Favored  : 82.98 %
  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:  1.01 (0.29), residues: 885
  helix:  2.31 (0.28), residues: 385
  sheet: -0.20 (0.39), residues: 177
  loop : -0.84 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.010   0.001   HIS A 220 
 PHE   0.011   0.001   PHE B 241 
 TYR   0.008   0.001   TYR R 316 
 ARG   0.005   0.000   ARG R 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03968 (  358)
  hydrogen bonds       : angle       4.22662 ( 1029)
  SS BOND              : bond        0.00423 (    2)
  SS BOND              : angle       0.78180 (    4)
  covalent geometry    : bond        0.00241 ( 6791)
  covalent geometry    : angle       0.47877 ( 9283)

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

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.803 
Fit side-chains
REVERT: R   82 MET cc_start: 0.7664 (ttt) cc_final: 0.7255 (ttp)
  outliers start: 14
  outliers final: 11
  residues processed: 107
  average time/residue: 0.1756
  time to fit residues: 25.8150
Evaluate side-chains
  101 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 70 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 85 optimal weight:    0.3980
   chunk 77 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
R 196 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.125320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.096446 restraints weight = 41792.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 5.97
r_work: 0.2972 rms_B_bonded: 5.81 restraints_weight: 2.0000
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2979
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    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 = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2979
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   6793  Z= 0.114
  Angle     :  0.471   7.493   9287  Z= 0.252
  Chirality :  0.040   0.140   1109
  Planarity :  0.003   0.038   1157
  Dihedral  : 10.420 166.950    989
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 15.24 %
    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:  1.06 (0.29), residues: 885
  helix:  2.33 (0.28), residues: 385
  sheet: -0.19 (0.39), residues: 177
  loop : -0.76 (0.32), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.011   0.001   PHE B 241 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.004   0.000   ARG R 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03889 (  358)
  hydrogen bonds       : angle       4.13388 ( 1029)
  SS BOND              : bond        0.01053 (    2)
  SS BOND              : angle       0.95570 (    4)
  covalent geometry    : bond        0.00254 ( 6791)
  covalent geometry    : angle       0.47090 ( 9283)

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

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.804 
Fit side-chains
REVERT: G   48 ASP cc_start: 0.8597 (p0) cc_final: 0.8322 (p0)
REVERT: R   82 MET cc_start: 0.7595 (ttt) cc_final: 0.7251 (ttp)
  outliers start: 17
  outliers final: 16
  residues processed: 107
  average time/residue: 0.1671
  time to fit residues: 24.8571
Evaluate side-chains
  104 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   95 LEU
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  227 LYS
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  294 ILE
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 81 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0770
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.0144

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

Flipped N/Q/H residues before XYZ refinement:
R 196 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.124873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.096670 restraints weight = 30533.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 4.55
r_work: 0.3015 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   6793  Z= 0.123
  Angle     :  0.476   7.034   9287  Z= 0.255
  Chirality :  0.040   0.139   1109
  Planarity :  0.003   0.038   1157
  Dihedral  : 10.062 170.863    989
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 15.07 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.29), residues: 885
  helix:  2.41 (0.28), residues: 379
  sheet: -0.15 (0.40), residues: 176
  loop : -0.74 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.012   0.001   PHE B 241 
 TYR   0.010   0.001   TYR A 358 
 ARG   0.004   0.000   ARG R 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03973 (  358)
  hydrogen bonds       : angle       4.09320 ( 1029)
  SS BOND              : bond        0.00295 (    2)
  SS BOND              : angle       0.93594 (    4)
  covalent geometry    : bond        0.00284 ( 6791)
  covalent geometry    : angle       0.47619 ( 9283)

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

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.763 
Fit side-chains
REVERT: G   48 ASP cc_start: 0.8557 (p0) cc_final: 0.8310 (p0)
REVERT: R   61 PHE cc_start: 0.7066 (m-10) cc_final: 0.6779 (m-10)
REVERT: R   82 MET cc_start: 0.7672 (ttt) cc_final: 0.7327 (ttp)
  outliers start: 22
  outliers final: 18
  residues processed: 104
  average time/residue: 0.1680
  time to fit residues: 24.2932
Evaluate side-chains
  104 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   95 LEU
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  227 LYS
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain R residue  294 ILE
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 87 optimal weight:    0.0470
   chunk 77 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.7480

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

Flipped N/Q/H residues before XYZ refinement:
R 196 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.125552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.097554 restraints weight = 46255.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 5.91
r_work: 0.2978 rms_B_bonded: 5.76 restraints_weight: 2.0000
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2987
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2987 r_free = 0.2987    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 = 0.2987 r_free = 0.2987    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2987
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6793  Z= 0.106
  Angle     :  0.463   6.906   9287  Z= 0.247
  Chirality :  0.040   0.139   1109
  Planarity :  0.003   0.037   1157
  Dihedral  :  9.742 174.709    989
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.56 %
    Favored  : 81.52 %
  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:  1.15 (0.29), residues: 885
  helix:  2.41 (0.28), residues: 379
  sheet: -0.09 (0.40), residues: 176
  loop : -0.70 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.009   0.001   TYR A 358 
 ARG   0.003   0.000   ARG R 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03745 (  358)
  hydrogen bonds       : angle       4.01598 ( 1029)
  SS BOND              : bond        0.00346 (    2)
  SS BOND              : angle       0.88704 (    4)
  covalent geometry    : bond        0.00235 ( 6791)
  covalent geometry    : angle       0.46313 ( 9283)

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

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 0.750 
Fit side-chains
REVERT: G   48 ASP cc_start: 0.8642 (p0) cc_final: 0.8352 (p0)
REVERT: R   61 PHE cc_start: 0.7018 (m-10) cc_final: 0.6714 (m-10)
REVERT: R   82 MET cc_start: 0.7698 (ttt) cc_final: 0.7339 (ttp)
  outliers start: 18
  outliers final: 17
  residues processed: 104
  average time/residue: 0.1765
  time to fit residues: 25.2261
Evaluate side-chains
  104 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   95 LEU
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  227 LYS
Chi-restraints excluded: chain R residue  294 ILE
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 18 optimal weight:    0.4980
   chunk 61 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0870
   chunk 53 optimal weight:    0.4980
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
B 239 ASN
R 196 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.126495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.098221 restraints weight = 38401.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 5.54
r_work: 0.3001 rms_B_bonded: 5.54 restraints_weight: 2.0000
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3010
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    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 = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3010
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6793  Z= 0.096
  Angle     :  0.457   6.783   9287  Z= 0.242
  Chirality :  0.039   0.139   1109
  Planarity :  0.003   0.036   1157
  Dihedral  :  9.387 177.691    989
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 15.88 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.29), residues: 885
  helix:  2.42 (0.28), residues: 380
  sheet: -0.05 (0.40), residues: 176
  loop : -0.63 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.008   0.001   TYR A 358 
 ARG   0.003   0.000   ARG R 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03471 (  358)
  hydrogen bonds       : angle       3.93256 ( 1029)
  SS BOND              : bond        0.00224 (    2)
  SS BOND              : angle       0.95285 (    4)
  covalent geometry    : bond        0.00207 ( 6791)
  covalent geometry    : angle       0.45685 ( 9283)

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

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.757 
Fit side-chains
REVERT: G   48 ASP cc_start: 0.8563 (p0) cc_final: 0.8274 (p0)
REVERT: R   61 PHE cc_start: 0.6874 (m-10) cc_final: 0.6586 (m-10)
REVERT: R   82 MET cc_start: 0.7618 (ttt) cc_final: 0.7274 (ttp)
  outliers start: 17
  outliers final: 15
  residues processed: 101
  average time/residue: 0.1707
  time to fit residues: 23.6217
Evaluate side-chains
  97 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0570
   chunk 20 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0070
   chunk 6 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.8120

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

Flipped N/Q/H residues before XYZ refinement:
R 196 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.126856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.098881 restraints weight = 27022.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 4.29
r_work: 0.3046 rms_B_bonded: 4.64 restraints_weight: 0.5000
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3054
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3054
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6793  Z= 0.109
  Angle     :  0.472   6.585   9287  Z= 0.250
  Chirality :  0.040   0.138   1109
  Planarity :  0.003   0.039   1157
  Dihedral  :  9.105 178.069    989
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.21 %
    Favored  : 81.20 %
  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:  1.23 (0.29), residues: 885
  helix:  2.44 (0.28), residues: 380
  sheet: -0.05 (0.40), residues: 176
  loop : -0.62 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 173 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.008   0.001   TYR A 358 
 ARG   0.003   0.000   ARG R 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03627 (  358)
  hydrogen bonds       : angle       3.92439 ( 1029)
  SS BOND              : bond        0.00311 (    2)
  SS BOND              : angle       0.97259 (    4)
  covalent geometry    : bond        0.00246 ( 6791)
  covalent geometry    : angle       0.47179 ( 9283)

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

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.737 
Fit side-chains
REVERT: G   48 ASP cc_start: 0.8523 (p0) cc_final: 0.8276 (p0)
REVERT: R   61 PHE cc_start: 0.6941 (m-10) cc_final: 0.6664 (m-10)
REVERT: R   82 MET cc_start: 0.7655 (ttt) cc_final: 0.7303 (ttp)
  outliers start: 16
  outliers final: 16
  residues processed: 96
  average time/residue: 0.1729
  time to fit residues: 22.9895
Evaluate side-chains
  99 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   95 LEU
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 8 optimal weight:    5.9990
   chunk 71 optimal weight:    0.0670
   chunk 39 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 23 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.9324

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

Flipped N/Q/H residues before XYZ refinement:
R 196 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.126192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.098736 restraints weight = 34806.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 5.37
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6793  Z= 0.117
  Angle     :  0.480   6.668   9287  Z= 0.254
  Chirality :  0.040   0.138   1109
  Planarity :  0.003   0.039   1157
  Dihedral  :  8.918 176.783    989
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.21 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.29), residues: 885
  helix:  2.44 (0.28), residues: 380
  sheet:  0.01 (0.40), residues: 176
  loop : -0.61 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 173 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.008   0.001   TYR A 358 
 ARG   0.003   0.000   ARG R 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03752 (  358)
  hydrogen bonds       : angle       3.91952 ( 1029)
  SS BOND              : bond        0.00322 (    2)
  SS BOND              : angle       0.96568 (    4)
  covalent geometry    : bond        0.00270 ( 6791)
  covalent geometry    : angle       0.47929 ( 9283)

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

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

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

  1770 Ramachandran restraints generated.
    885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.806 
Fit side-chains
REVERT: R   61 PHE cc_start: 0.7095 (m-10) cc_final: 0.6812 (m-10)
REVERT: R   82 MET cc_start: 0.7677 (ttt) cc_final: 0.7359 (ttp)
  outliers start: 17
  outliers final: 16
  residues processed: 96
  average time/residue: 0.1744
  time to fit residues: 23.1608
Evaluate side-chains
  99 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   95 LEU
Chi-restraints excluded: chain R residue  113 ASP
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  196 ASN
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
R  51 ASN
R 196 ASN
R 312 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.124478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.096881 restraints weight = 23644.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 4.07
r_work: 0.3018 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3027
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3027
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6793  Z= 0.154
  Angle     :  0.502   6.763   9287  Z= 0.268
  Chirality :  0.041   0.138   1109
  Planarity :  0.003   0.041   1157
  Dihedral  :  8.821 174.303    989
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.05 %
    Favored  : 81.20 %
  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:  1.21 (0.29), residues: 885
  helix:  2.39 (0.28), residues: 380
  sheet: -0.03 (0.40), residues: 178
  loop : -0.61 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 173 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.015   0.001   PHE B 241 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.003   0.000   ARG R 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04239 (  358)
  hydrogen bonds       : angle       4.00625 ( 1029)
  SS BOND              : bond        0.00367 (    2)
  SS BOND              : angle       1.02544 (    4)
  covalent geometry    : bond        0.00366 ( 6791)
  covalent geometry    : angle       0.50143 ( 9283)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4148.61 seconds
wall clock time: 74 minutes 1.63 seconds (4441.63 seconds total)