Starting phenix.real_space_refine
on Tue Feb  3 21:04:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ll8_63193/02_2026/9ll8_63193.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ll8_63193/02_2026/9ll8_63193.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ll8_63193/02_2026/9ll8_63193.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ll8_63193/02_2026/9ll8_63193.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ll8_63193/02_2026/9ll8_63193.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ll8_63193/02_2026/9ll8_63193.cif"
  }
  resolution = 2.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=  -0.001 sd=   0.031
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: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    4425      2.51       5
     N    1161      2.21       5
     O    1287      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6926
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2611
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 445
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "A"
      Number of atoms: 1824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1824
          Classifications: {'peptide': 226}
          Link IDs: {'PTRANS': 2, 'TRANS': 223}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 1993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 1993
          Classifications: {'peptide': 258}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 9, 'TRANS': 248}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "R"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 53
          Unusual residues: {'91Q': 1, 'CLR': 1}
          Classifications: {'undetermined': 2, 'water': 10}
          Link IDs: {None: 11}
  Time building chain proxies: 1.40, per 1000 atoms: 0.20
  Number of scatterers: 6926
  At special positions: 0
  Unit cell: (78, 101.25, 130.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    1287      8.00
     N    1161      7.00
     C    4425      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 148 " - pdb=" SG  CYS R 227 " 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: 0.63
  Conformation dependent library (CDL) restraints added in 230.1 milliseconds
  

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1670

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 9 sheets defined
      45.0% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'B' and resid 1 through 25
      removed outlier: 3.734A  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 'C' and resid 7 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'A' and resid 6 through 30
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 3.735A  pdb=" N   PHE A 215 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.548A  pdb=" N   PHE A 274 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 329 through 351
      removed outlier: 3.570A  pdb=" N   LYS A 349 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 81 through 102
    Processing helix  chain 'R' and resid 107 through 127
    Processing helix  chain 'R' and resid 127 through 137
      removed outlier: 3.533A  pdb=" N   LEU R 136 " --> pdb=" O   MET R 132 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 147 through 179
    Processing helix  chain 'R' and resid 179 through 186
    Processing helix  chain 'R' and resid 188 through 207
      removed outlier: 3.912A  pdb=" N   ALA R 192 " --> pdb=" O   SER R 188 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 215
      removed outlier: 3.672A  pdb=" N   VAL R 212 " --> pdb=" O   MET R 208 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU R 215 " --> pdb=" O   PRO R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 232 through 243
    Processing helix  chain 'R' and resid 243 through 261
    Processing helix  chain 'R' and resid 316 through 349
      Proline residue:  R 338  - end of helix
      removed outlier: 3.613A  pdb=" N   VAL R 347 " --> pdb=" O   ASN R 343 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 355 through 381
      removed outlier: 3.849A  pdb=" N   LEU R 362 " --> pdb=" O   ILE R 358 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   TRP R 367 " --> pdb=" O   ASN R 363 " (cutoff:3.500A)
      Proline residue:  R 377  - end of helix
    Processing helix  chain 'R' and resid 384 through 392
    Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.252A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL B 327 " --> pdb=" O   TRP B 339 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.102A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL B  71 " --> pdb=" O   HIS B  62 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.771A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.539A  pdb=" N   ALA B 167 " --> pdb=" O   THR B 159 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.519A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLY B 202 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.301A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.812A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   PHE B 253 " --> pdb=" O   PHE B 241 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   THR B 243 " --> pdb=" O   ARG B 251 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ARG B 251 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 5.154A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   LEU B 252 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.672A  pdb=" N   ALA B 287 " --> pdb=" O   ASN B 295 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   TYR B 289 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.751A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.681A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.591A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.985A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 222 through 223

    357 hydrogen bonds defined for protein.
    1044 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: 0.72

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1131
        1.32 -     1.44: 1878
        1.44 -     1.56: 3965
        1.56 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 7052
  Sorted by residual:
  bond pdb=" C   ASN R 354 "
       pdb=" O   ASN R 354 "
    ideal  model  delta    sigma   weight residual
    1.231  1.310 -0.079 2.00e-02 2.50e+03 1.58e+01
  bond pdb=" N   ILE R 358 "
       pdb=" CA  ILE R 358 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.040 1.25e-02 6.40e+03 1.05e+01
  bond pdb=" C   GLY R 359 "
       pdb=" O   GLY R 359 "
    ideal  model  delta    sigma   weight residual
    1.235  1.191  0.044 1.35e-02 5.49e+03 1.04e+01
  bond pdb=" C   LYS R 220 "
       pdb=" O   LYS R 220 "
    ideal  model  delta    sigma   weight residual
    1.236  1.195  0.041 1.38e-02 5.25e+03 8.83e+00
  bond pdb=" N   VAL R 357 "
       pdb=" CA  VAL R 357 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.17e-02 7.31e+03 8.78e+00
  ... (remaining 7047 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 9041
        1.35 -     2.71: 427
        2.71 -     4.06: 60
        4.06 -     5.41: 24
        5.41 -     6.77: 6
  Bond angle restraints: 9558
  Sorted by residual:
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     113.20  108.79    4.41 9.60e-01 1.09e+00 2.11e+01
  angle pdb=" C   GLY R 359 "
        pdb=" N   ALA R 360 "
        pdb=" CA  ALA R 360 "
      ideal   model   delta    sigma   weight residual
     120.28  124.81   -4.53 1.34e+00 5.57e-01 1.14e+01
  angle pdb=" C   ASP R 217 "
        pdb=" N   ASP R 218 "
        pdb=" CA  ASP R 218 "
      ideal   model   delta    sigma   weight residual
     121.54  127.75   -6.21 1.91e+00 2.74e-01 1.06e+01
  angle pdb=" CA  VAL R 357 "
        pdb=" C   VAL R 357 "
        pdb=" O   VAL R 357 "
      ideal   model   delta    sigma   weight residual
     121.17  117.94    3.23 1.06e+00 8.90e-01 9.30e+00
  angle pdb=" CA  THR R 381 "
        pdb=" C   THR R 381 "
        pdb=" O   THR R 381 "
      ideal   model   delta    sigma   weight residual
     120.32  117.24    3.08 1.02e+00 9.61e-01 9.10e+00
  ... (remaining 9553 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.16: 4144
       31.16 -    62.32: 88
       62.32 -    93.48: 9
       93.48 -   124.64: 0
      124.64 -   155.80: 2
  Dihedral angle restraints: 4243
    sinusoidal: 1674
      harmonic: 2569
  Sorted by residual:
  dihedral pdb=" CB  CYS R 148 "
           pdb=" SG  CYS R 148 "
           pdb=" SG  CYS R 227 "
           pdb=" CB  CYS R 227 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -155.47   69.47     1      1.00e+01 1.00e-02 6.23e+01
  dihedral pdb=" C1  91Q R 501 "
           pdb=" C3  91Q R 501 "
           pdb=" N1  91Q R 501 "
           pdb=" C4  91Q R 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     198.00   42.20  155.80     1      3.00e+01 1.11e-03 2.04e+01
  dihedral pdb=" C2  91Q R 501 "
           pdb=" C3  91Q R 501 "
           pdb=" N1  91Q R 501 "
           pdb=" C4  91Q R 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      73.77  -79.80  153.57     1      3.00e+01 1.11e-03 2.02e+01
  ... (remaining 4240 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 743
       0.040 -    0.079: 259
       0.079 -    0.119: 86
       0.119 -    0.159: 20
       0.159 -    0.199: 3
  Chirality restraints: 1111
  Sorted by residual:
  chirality pdb=" C13 CLR R 502 "
            pdb=" C12 CLR R 502 "
            pdb=" C14 CLR R 502 "
            pdb=" C17 CLR R 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.73   -0.20 2.00e-01 2.50e+01 9.86e-01
  chirality pdb=" C10 CLR R 502 "
            pdb=" C1  CLR R 502 "
            pdb=" C5  CLR R 502 "
            pdb=" C9  CLR R 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.68   -0.17 2.00e-01 2.50e+01 6.84e-01
  chirality pdb=" CA  ILE A 265 "
            pdb=" N   ILE A 265 "
            pdb=" C   ILE A 265 "
            pdb=" CB  ILE A 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.58e-01
  ... (remaining 1108 not shown)

  Planarity restraints: 1195
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP R 218 "   -0.010 2.00e-02 2.50e+03   1.95e-02 3.81e+00
        pdb=" C   ASP R 218 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ASP R 218 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER R 219 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.026 5.00e-02 4.00e+02   3.98e-02 2.53e+00
        pdb=" N   PRO B 236 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C  54 "    0.026 5.00e-02 4.00e+02   3.97e-02 2.52e+00
        pdb=" N   PRO C  55 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO C  55 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C  55 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1192 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 682
        2.74 -     3.28: 6658
        3.28 -     3.82: 11176
        3.82 -     4.36: 13214
        4.36 -     4.90: 23124
  Nonbonded interactions: 54854
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A  33 "
            pdb=" NZ  LYS A 197 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" NZ  LYS R 195 "
            pdb=" O   HOH R 601 "
     model   vdw
     2.226 3.120
  nonbonded pdb=" O   TYR R 139 "
            pdb=" OG  SER R 226 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OH  TYR A 230 "
            pdb=" OG  SER A 281 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG1 THR A 190 "
            pdb=" O   LEU A 194 "
     model   vdw
     2.275 3.040
  ... (remaining 54849 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.400
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:5.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5207
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   0.079   7053  Z= 0.236
  Angle     :  0.673   6.768   9560  Z= 0.388
  Chirality :  0.046   0.199   1111
  Planarity :  0.004   0.045   1195
  Dihedral  : 13.355 155.802   2570
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.28), residues: 868
  helix:  1.75 (0.28), residues: 372
  sheet:  0.56 (0.43), residues: 146
  loop : -1.12 (0.30), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 251 
 TYR   0.016   0.001   TYR R 139 
 PHE   0.019   0.002   PHE B 253 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.002   0.001   HIS R 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 7052)
  covalent geometry    : angle       0.67271 ( 9558)
  SS BOND              : bond        0.00175 (    1)
  SS BOND              : angle       2.34064 (    2)
  hydrogen bonds       : bond        0.20345 (  357)
  hydrogen bonds       : angle       6.78344 ( 1044)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.170 
Fit side-chains
REVERT: B   42 ARG cc_start: 0.6934 (mmm160) cc_final: 0.5754 (mmp-170)
REVERT: B  173 THR cc_start: 0.7616 (m) cc_final: 0.7221 (m)
REVERT: B  217 MET cc_start: 0.7428 (pmm) cc_final: 0.7184 (pp-130)
REVERT: B  219 ARG cc_start: 0.7083 (mtp85) cc_final: 0.6808 (mtp180)
REVERT: A  298 GLU cc_start: 0.6907 (tm-30) cc_final: 0.6545 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.4065
  time to fit residues: 64.9070
Evaluate side-chains
  88 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.0070
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.1402

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

Flipped N/Q/H residues before XYZ refinement:
B 225 HIS
B 237 ASN
B 295 ASN
B 340 ASN
A 188 HIS
R 178 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.221288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.165673 restraints weight = 7551.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3905 rms_B_bonded: 1.94
r_work: 0.3808 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3698 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7053  Z= 0.168
  Angle     :  0.662  11.597   9560  Z= 0.345
  Chirality :  0.046   0.139   1111
  Planarity :  0.004   0.036   1195
  Dihedral  :  7.848 131.580   1009
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 10.56 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.28), residues: 868
  helix:  2.03 (0.27), residues: 381
  sheet:  1.10 (0.39), residues: 166
  loop : -1.36 (0.32), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 314 
 TYR   0.015   0.002   TYR R 174 
 PHE   0.019   0.002   PHE A 189 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.009   0.002   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 7052)
  covalent geometry    : angle       0.66224 ( 9558)
  SS BOND              : bond        0.00067 (    1)
  SS BOND              : angle       0.52953 (    2)
  hydrogen bonds       : bond        0.05209 (  357)
  hydrogen bonds       : angle       4.70750 ( 1044)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.6714 (ptp90)
REVERT: B  134 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.6343 (ppt170)
REVERT: B  217 MET cc_start: 0.8250 (pmm) cc_final: 0.8012 (pp-130)
REVERT: A   29 LYS cc_start: 0.7824 (tttp) cc_final: 0.7387 (tptt)
REVERT: A  252 SER cc_start: 0.7939 (t) cc_final: 0.7688 (p)
REVERT: R  259 LYS cc_start: 0.6330 (tttt) cc_final: 0.6109 (ttpt)
REVERT: R  335 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7439 (mtt)
  outliers start: 23
  outliers final: 4
  residues processed: 108
  average time/residue: 0.4955
  time to fit residues: 56.3590
Evaluate side-chains
  87 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  335 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 67 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 53 optimal weight:    5.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 225 HIS
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.216980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.160305 restraints weight = 7475.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3857 rms_B_bonded: 1.96
r_work: 0.3759 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3645 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.4037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7053  Z= 0.123
  Angle     :  0.539  10.998   9560  Z= 0.284
  Chirality :  0.042   0.136   1111
  Planarity :  0.003   0.037   1195
  Dihedral  :  7.237 123.225   1009
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 14.71 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.28), residues: 868
  helix:  2.31 (0.26), residues: 380
  sheet:  0.94 (0.39), residues: 167
  loop : -1.25 (0.32), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  21 
 TYR   0.009   0.001   TYR R 139 
 PHE   0.016   0.001   PHE B 151 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 7052)
  covalent geometry    : angle       0.53899 ( 9558)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.52787 (    2)
  hydrogen bonds       : bond        0.04573 (  357)
  hydrogen bonds       : angle       4.35550 ( 1044)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 83
  time to evaluate  : 0.252 
Fit side-chains
REVERT: B  134 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.6639 (ppt170)
REVERT: B  217 MET cc_start: 0.8291 (pmm) cc_final: 0.8088 (pp-130)
REVERT: A   21 ARG cc_start: 0.7433 (mtm180) cc_final: 0.7204 (mtm180)
REVERT: A   29 LYS cc_start: 0.7882 (tttp) cc_final: 0.7336 (tptt)
REVERT: A  205 ARG cc_start: 0.7320 (ptt-90) cc_final: 0.7022 (mmt-90)
REVERT: A  313 ARG cc_start: 0.7646 (mtt-85) cc_final: 0.7368 (mtt180)
REVERT: A  329 THR cc_start: 0.7216 (OUTLIER) cc_final: 0.7007 (t)
REVERT: R  259 LYS cc_start: 0.6585 (tttt) cc_final: 0.6303 (ttpt)
REVERT: R  335 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7509 (mtt)
  outliers start: 23
  outliers final: 11
  residues processed: 93
  average time/residue: 0.4293
  time to fit residues: 42.2514
Evaluate side-chains
  88 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain R residue  170 SER
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  197 ILE
Chi-restraints excluded: chain R residue  335 MET
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 81 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0870
   chunk 29 optimal weight:    7.9990
   chunk 7 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    1.0962

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

Flipped N/Q/H residues before XYZ refinement:
B 225 HIS
B 340 ASN
A  22 ASN
A 322 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.213513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.155838 restraints weight = 7541.859|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 1.96
r_work: 0.3706 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3591 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.4564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7053  Z= 0.137
  Angle     :  0.560   9.402   9560  Z= 0.295
  Chirality :  0.043   0.140   1111
  Planarity :  0.003   0.035   1195
  Dihedral  :  6.939 114.507   1009
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 15.11 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.28), residues: 868
  helix:  2.36 (0.26), residues: 380
  sheet:  0.91 (0.40), residues: 165
  loop : -1.25 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  24 
 TYR   0.009   0.001   TYR R 174 
 PHE   0.018   0.002   PHE B 151 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7052)
  covalent geometry    : angle       0.56025 ( 9558)
  SS BOND              : bond        0.00088 (    1)
  SS BOND              : angle       0.52378 (    2)
  hydrogen bonds       : bond        0.04671 (  357)
  hydrogen bonds       : angle       4.31673 ( 1044)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 80
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: B  134 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.6953 (ppt170)
REVERT: B  217 MET cc_start: 0.8405 (pmm) cc_final: 0.8102 (pp-130)
REVERT: C   32 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7802 (ttpp)
REVERT: A   29 LYS cc_start: 0.7912 (tttp) cc_final: 0.7378 (tptt)
REVERT: A  205 ARG cc_start: 0.7362 (ptt-90) cc_final: 0.7029 (mmt-90)
REVERT: A  318 GLU cc_start: 0.5607 (tp30) cc_final: 0.5180 (tp30)
REVERT: A  329 THR cc_start: 0.7263 (OUTLIER) cc_final: 0.7045 (t)
REVERT: A  341 ASP cc_start: 0.8231 (t0) cc_final: 0.7963 (t0)
REVERT: R  259 LYS cc_start: 0.6739 (tttt) cc_final: 0.6361 (tttt)
REVERT: R  330 PHE cc_start: 0.7155 (m-80) cc_final: 0.6942 (m-10)
  outliers start: 26
  outliers final: 14
  residues processed: 91
  average time/residue: 0.5366
  time to fit residues: 51.6431
Evaluate side-chains
  94 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue   32 LYS
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  197 ILE
Chi-restraints excluded: chain R residue  204 VAL
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 58 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
C  59 ASN
A  22 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.213211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.155061 restraints weight = 7480.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3794 rms_B_bonded: 1.97
r_work: 0.3691 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3579 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.4846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7053  Z= 0.129
  Angle     :  0.538   9.368   9560  Z= 0.285
  Chirality :  0.043   0.132   1111
  Planarity :  0.003   0.037   1195
  Dihedral  :  6.348  97.932   1009
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 15.64 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.28), residues: 868
  helix:  2.42 (0.26), residues: 380
  sheet:  0.80 (0.40), residues: 170
  loop : -1.22 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  21 
 TYR   0.007   0.001   TYR R 174 
 PHE   0.017   0.001   PHE B 151 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.002   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7052)
  covalent geometry    : angle       0.53835 ( 9558)
  SS BOND              : bond        0.00131 (    1)
  SS BOND              : angle       0.45270 (    2)
  hydrogen bonds       : bond        0.04460 (  357)
  hydrogen bonds       : angle       4.24293 ( 1044)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 86
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.6689 (ptp90)
REVERT: B  134 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7120 (ppt170)
REVERT: B  217 MET cc_start: 0.8339 (pmm) cc_final: 0.8102 (pp-130)
REVERT: A  205 ARG cc_start: 0.7344 (ptt-90) cc_final: 0.7057 (mmt-90)
REVERT: A  221 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7735 (mt)
REVERT: R  259 LYS cc_start: 0.6734 (tttt) cc_final: 0.6418 (ttpt)
REVERT: R  330 PHE cc_start: 0.7183 (m-80) cc_final: 0.6943 (m-10)
REVERT: R  335 MET cc_start: 0.7787 (mmt) cc_final: 0.7504 (mtt)
  outliers start: 27
  outliers final: 10
  residues processed: 101
  average time/residue: 0.4985
  time to fit residues: 53.1246
Evaluate side-chains
  91 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  197 ILE
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 51 optimal weight:    0.3980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 340 ASN
C  59 ASN
A  22 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.213768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.156011 restraints weight = 7542.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3802 rms_B_bonded: 1.96
r_work: 0.3701 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3590 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.5010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7053  Z= 0.116
  Angle     :  0.515   8.044   9560  Z= 0.276
  Chirality :  0.042   0.179   1111
  Planarity :  0.003   0.037   1195
  Dihedral  :  5.834  80.553   1009
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 16.58 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.29), residues: 868
  helix:  2.49 (0.26), residues: 379
  sheet:  0.83 (0.40), residues: 170
  loop : -1.17 (0.32), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  21 
 TYR   0.006   0.001   TYR R 153 
 PHE   0.015   0.001   PHE B 151 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.002   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 7052)
  covalent geometry    : angle       0.51522 ( 9558)
  SS BOND              : bond        0.00169 (    1)
  SS BOND              : angle       0.33373 (    2)
  hydrogen bonds       : bond        0.04125 (  357)
  hydrogen bonds       : angle       4.17720 ( 1044)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 81
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6632 (ptp90)
REVERT: B  134 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7081 (ppt170)
REVERT: B  217 MET cc_start: 0.8374 (pmm) cc_final: 0.8148 (pp-130)
REVERT: B  290 ASP cc_start: 0.7869 (p0) cc_final: 0.7566 (p0)
REVERT: A  205 ARG cc_start: 0.7357 (ptt-90) cc_final: 0.7062 (mmt-90)
REVERT: A  221 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7739 (mt)
REVERT: A  341 ASP cc_start: 0.8222 (t0) cc_final: 0.7949 (t70)
REVERT: R  259 LYS cc_start: 0.6823 (tttt) cc_final: 0.6492 (ttpt)
REVERT: R  330 PHE cc_start: 0.7136 (m-80) cc_final: 0.6844 (m-10)
  outliers start: 29
  outliers final: 11
  residues processed: 101
  average time/residue: 0.5208
  time to fit residues: 55.7392
Evaluate side-chains
  92 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  197 ILE
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 40 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
B  54 HIS
B 239 ASN
B 340 ASN
C  59 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.210081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.150739 restraints weight = 7491.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 1.95
r_work: 0.3623 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3509 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.5240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7053  Z= 0.189
  Angle     :  0.635  13.147   9560  Z= 0.333
  Chirality :  0.046   0.174   1111
  Planarity :  0.004   0.037   1195
  Dihedral  :  6.285  85.812   1009
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 16.84 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.28), residues: 868
  helix:  2.24 (0.26), residues: 381
  sheet:  0.69 (0.39), residues: 165
  loop : -1.30 (0.31), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  21 
 TYR   0.008   0.002   TYR B  59 
 PHE   0.022   0.002   PHE B 151 
 TRP   0.017   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 7052)
  covalent geometry    : angle       0.63544 ( 9558)
  SS BOND              : bond        0.00279 (    1)
  SS BOND              : angle       0.29551 (    2)
  hydrogen bonds       : bond        0.05397 (  357)
  hydrogen bonds       : angle       4.41603 ( 1044)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 85
  time to evaluate  : 0.277 
Fit side-chains
REVERT: B   52 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.6783 (ptp90)
REVERT: B  134 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7278 (ppt170)
REVERT: B  217 MET cc_start: 0.8459 (pmm) cc_final: 0.8206 (pp-130)
REVERT: A   20 ASP cc_start: 0.8143 (m-30) cc_final: 0.7885 (t0)
REVERT: A  205 ARG cc_start: 0.7379 (ptt-90) cc_final: 0.7046 (mmt-90)
REVERT: A  221 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7767 (mt)
REVERT: A  262 THR cc_start: 0.7686 (t) cc_final: 0.7092 (m)
REVERT: A  341 ASP cc_start: 0.8315 (t0) cc_final: 0.8004 (t70)
REVERT: R  259 LYS cc_start: 0.6869 (tttt) cc_final: 0.6454 (ttpt)
REVERT: R  330 PHE cc_start: 0.7279 (m-80) cc_final: 0.6955 (m-10)
  outliers start: 31
  outliers final: 16
  residues processed: 106
  average time/residue: 0.5520
  time to fit residues: 61.8800
Evaluate side-chains
  99 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  197 ILE
Chi-restraints excluded: chain R residue  204 VAL
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  239 SER
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 20 optimal weight:    0.0010
   chunk 43 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 83 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.6586

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
A  22 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.213681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.156035 restraints weight = 7549.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3826 rms_B_bonded: 1.95
r_work: 0.3725 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3614 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.5306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7053  Z= 0.110
  Angle     :  0.507   5.499   9560  Z= 0.275
  Chirality :  0.042   0.163   1111
  Planarity :  0.003   0.038   1195
  Dihedral  :  5.870  82.746   1009
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.25 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.29), residues: 868
  helix:  2.50 (0.26), residues: 380
  sheet:  0.73 (0.40), residues: 170
  loop : -1.16 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 214 
 TYR   0.007   0.001   TYR R 153 
 PHE   0.015   0.001   PHE B 151 
 TRP   0.014   0.002   TRP B  82 
 HIS   0.002   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 7052)
  covalent geometry    : angle       0.50677 ( 9558)
  SS BOND              : bond        0.00184 (    1)
  SS BOND              : angle       0.36705 (    2)
  hydrogen bonds       : bond        0.04048 (  357)
  hydrogen bonds       : angle       4.16475 ( 1044)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.278 
Fit side-chains
REVERT: B  134 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7175 (ppt170)
REVERT: B  212 ASP cc_start: 0.8417 (t70) cc_final: 0.8180 (t70)
REVERT: B  217 MET cc_start: 0.8468 (pmm) cc_final: 0.8216 (pp-130)
REVERT: B  290 ASP cc_start: 0.7852 (p0) cc_final: 0.7562 (p0)
REVERT: A   20 ASP cc_start: 0.8045 (m-30) cc_final: 0.7837 (t0)
REVERT: A  205 ARG cc_start: 0.7316 (ptt-90) cc_final: 0.7060 (mmt-90)
REVERT: A  221 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7785 (mt)
REVERT: A  240 MET cc_start: 0.3102 (ptp) cc_final: 0.2718 (ptm)
REVERT: R  330 PHE cc_start: 0.7118 (m-80) cc_final: 0.6854 (m-10)
  outliers start: 19
  outliers final: 13
  residues processed: 93
  average time/residue: 0.5182
  time to fit residues: 51.1352
Evaluate side-chains
  91 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  197 ILE
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 78 optimal weight:    0.5980
   chunk 54 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0970
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.214093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.156664 restraints weight = 7485.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 1.94
r_work: 0.3711 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3600 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.5364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7053  Z= 0.108
  Angle     :  0.500   5.789   9560  Z= 0.270
  Chirality :  0.042   0.154   1111
  Planarity :  0.003   0.039   1195
  Dihedral  :  5.617  74.966   1009
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.79 %
    Favored  : 77.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.29), residues: 868
  helix:  2.59 (0.26), residues: 381
  sheet:  0.73 (0.40), residues: 170
  loop : -1.05 (0.32), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 214 
 TYR   0.006   0.001   TYR R 153 
 PHE   0.014   0.001   PHE A 189 
 TRP   0.014   0.002   TRP B  82 
 HIS   0.002   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 7052)
  covalent geometry    : angle       0.50008 ( 9558)
  SS BOND              : bond        0.00126 (    1)
  SS BOND              : angle       0.34111 (    2)
  hydrogen bonds       : bond        0.03938 (  357)
  hydrogen bonds       : angle       4.12676 ( 1044)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.280 
Fit side-chains
REVERT: B   52 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.6599 (ptp90)
REVERT: B  134 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7110 (ppt170)
REVERT: B  217 MET cc_start: 0.8470 (pmm) cc_final: 0.8169 (pp-130)
REVERT: B  290 ASP cc_start: 0.7825 (p0) cc_final: 0.7566 (p0)
REVERT: A   20 ASP cc_start: 0.8050 (m-30) cc_final: 0.7843 (t0)
REVERT: A  205 ARG cc_start: 0.7346 (ptt-90) cc_final: 0.7094 (mmt-90)
REVERT: A  221 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7742 (mt)
REVERT: A  240 MET cc_start: 0.3097 (OUTLIER) cc_final: 0.2683 (ptm)
REVERT: A  262 THR cc_start: 0.7555 (t) cc_final: 0.7039 (m)
REVERT: R  330 PHE cc_start: 0.7069 (m-80) cc_final: 0.6786 (m-10)
  outliers start: 19
  outliers final: 14
  residues processed: 96
  average time/residue: 0.5720
  time to fit residues: 58.0622
Evaluate side-chains
  96 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  197 ILE
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 61 optimal weight:    0.0000
   chunk 69 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   overall best weight:    0.7786

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.213705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.155943 restraints weight = 7541.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 1.96
r_work: 0.3696 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3585 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.5428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7053  Z= 0.113
  Angle     :  0.510   6.078   9560  Z= 0.276
  Chirality :  0.042   0.150   1111
  Planarity :  0.003   0.039   1195
  Dihedral  :  5.601  72.680   1009
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.79 %
    Favored  : 77.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.29), residues: 868
  helix:  2.58 (0.26), residues: 381
  sheet:  0.71 (0.40), residues: 170
  loop : -1.02 (0.32), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 214 
 TYR   0.006   0.001   TYR R 153 
 PHE   0.014   0.001   PHE B 151 
 TRP   0.024   0.002   TRP R 336 
 HIS   0.002   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 7052)
  covalent geometry    : angle       0.51018 ( 9558)
  SS BOND              : bond        0.00151 (    1)
  SS BOND              : angle       0.31310 (    2)
  hydrogen bonds       : bond        0.03998 (  357)
  hydrogen bonds       : angle       4.20377 ( 1044)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.169 
Fit side-chains
REVERT: B   52 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.6627 (ptp90)
REVERT: B  134 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7113 (ppt170)
REVERT: B  217 MET cc_start: 0.8486 (pmm) cc_final: 0.8190 (pp-130)
REVERT: B  290 ASP cc_start: 0.7847 (p0) cc_final: 0.7587 (p0)
REVERT: A  205 ARG cc_start: 0.7354 (ptt-90) cc_final: 0.7100 (mmt-90)
REVERT: A  221 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7747 (mt)
REVERT: A  240 MET cc_start: 0.3094 (OUTLIER) cc_final: 0.2670 (ptm)
REVERT: A  262 THR cc_start: 0.7602 (t) cc_final: 0.7075 (m)
REVERT: R  330 PHE cc_start: 0.7093 (m-80) cc_final: 0.6783 (m-10)
  outliers start: 19
  outliers final: 14
  residues processed: 99
  average time/residue: 0.5127
  time to fit residues: 53.5755
Evaluate side-chains
  98 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  227 SER
Chi-restraints excluded: chain B residue  254 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain R residue  188 SER
Chi-restraints excluded: chain R residue  197 ILE
Chi-restraints excluded: chain R residue  258 ILE
Chi-restraints excluded: chain R residue  379 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0000
   chunk 72 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.7788

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.213515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.155857 restraints weight = 7483.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3800 rms_B_bonded: 1.95
r_work: 0.3695 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3585 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.5431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7053  Z= 0.115
  Angle     :  0.517   5.993   9560  Z= 0.281
  Chirality :  0.042   0.147   1111
  Planarity :  0.003   0.039   1195
  Dihedral  :  5.539  71.310   1009
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 19.92 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.29), residues: 868
  helix:  2.55 (0.26), residues: 380
  sheet:  0.72 (0.40), residues: 170
  loop : -1.03 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 214 
 TYR   0.006   0.001   TYR R 153 
 PHE   0.014   0.001   PHE B 151 
 TRP   0.015   0.002   TRP R 336 
 HIS   0.003   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 7052)
  covalent geometry    : angle       0.51673 ( 9558)
  SS BOND              : bond        0.00136 (    1)
  SS BOND              : angle       0.32538 (    2)
  hydrogen bonds       : bond        0.04035 (  357)
  hydrogen bonds       : angle       4.21243 ( 1044)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3405.72 seconds
wall clock time: 58 minutes 38.20 seconds (3518.20 seconds total)