Starting phenix.real_space_refine
on Tue Mar  3 16:14:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dhr_30682/03_2026/7dhr_30682.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dhr_30682/03_2026/7dhr_30682.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dhr_30682/03_2026/7dhr_30682.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dhr_30682/03_2026/7dhr_30682.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dhr_30682/03_2026/7dhr_30682.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dhr_30682/03_2026/7dhr_30682.cif"
  }
  resolution = 3.8
  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=   0.000 sd=   0.007
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      42      5.16       5
     C    4538      2.51       5
     N    1206      2.21       5
     O    1271      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7057
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1495
          Classifications: {'peptide': 194}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 4, 'TRANS': 189}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 168
          Unresolved non-hydrogen angles: 204
          Unresolved non-hydrogen dihedrals: 139
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 3, 'ARG:plan': 8, 'GLU:plan': 8, 'ASN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 127
    Chain: "B"
      Number of atoms: 2301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2301
          Classifications: {'peptide': 327}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 55}
          Link IDs: {'PTRANS': 5, 'TRANS': 321}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 210
          Unresolved non-hydrogen angles: 258
          Unresolved non-hydrogen dihedrals: 162
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ARG:plan': 14, 'GLN:plan1': 6, 'GLU:plan': 6, 'ASP:plan': 13, 'ASN:plan1': 4}
          Unresolved non-hydrogen planarities: 169
    Chain: "G"
      Number of atoms: 317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 317
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 4, 'TRANS': 44}
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 48
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "N"
      Number of atoms: 851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 851
          Classifications: {'peptide': 123}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 5, 'TRANS': 117}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 92
          Unresolved non-hydrogen angles: 113
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 58
    Chain: "R"
      Number of atoms: 2078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2078
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'PTRANS': 7, 'TRANS': 276}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 229
          Unresolved non-hydrogen angles: 292
          Unresolved non-hydrogen dihedrals: 196
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLU:plan': 7, 'TRP:plan': 2, 'PHE:plan': 4, 'TYR:plan': 2, 'GLN:plan1': 5, 'ASN:plan1': 4, 'ARG:plan': 5, 'HIS:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 149
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'5FW': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.44, per 1000 atoms: 0.20
  Number of scatterers: 7057
  At special positions: 0
  Unit cell: (82.134, 98.358, 120.666, 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      42     16.00
     O    1271      8.00
     N    1206      7.00
     C    4538      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=2.04

  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: 0.68
  Conformation dependent library (CDL) restraints added in 324.3 milliseconds
  

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1844

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 11 sheets defined
      29.0% alpha, 12.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 24
      removed outlier: 3.592A  pdb=" N   GLN A  19 " --> pdb=" O   GLU A  15 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLU A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ALA A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 32
    Processing helix  chain 'A' and resid 33 through 38
    Processing helix  chain 'A' and resid 265 through 269
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 295 through 300
      removed outlier: 3.755A  pdb=" N   LYS A 300 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.952A  pdb=" N   PHE A 315 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 312 through 316'
    Processing helix  chain 'A' and resid 331 through 345
      removed outlier: 3.516A  pdb=" N   ARG A 336 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   ALA A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   TYR A 339 " --> pdb=" O   THR A 335 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   PHE A 340 " --> pdb=" O   ARG A 336 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 350
      removed outlier: 3.819A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   THR A 350 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 345 through 350'
    Processing helix  chain 'A' and resid 372 through 390
      removed outlier: 3.914A  pdb=" N   ASP A 378 " --> pdb=" O   ARG A 374 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   ASP A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG A 389 " --> pdb=" O   ARG A 385 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLN A 390 " --> pdb=" O   MET A 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 13 through 25
      removed outlier: 3.721A  pdb=" N   ILE B  18 " --> pdb=" O   LEU B  14 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 19 through 24
    Processing helix  chain 'G' and resid 29 through 34
    Processing helix  chain 'G' and resid 34 through 44
      removed outlier: 3.697A  pdb=" N   ALA G  43 " --> pdb=" O   ALA G  39 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.918A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'R' and resid 31 through 49
      removed outlier: 3.520A  pdb=" N   MET R  36 " --> pdb=" O   TRP R  32 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   SER R  41 " --> pdb=" O   GLY R  37 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE R  43 " --> pdb=" O   VAL R  39 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   VAL R  44 " --> pdb=" O   MET R  40 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   LEU R  45 " --> pdb=" O   SER R  41 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL R  48 " --> pdb=" O   VAL R  44 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 70
    Processing helix  chain 'R' and resid 71 through 76
    Processing helix  chain 'R' and resid 77 through 86
      removed outlier: 4.055A  pdb=" N   MET R  82 " --> pdb=" O   ALA R  78 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 88 through 93
      removed outlier: 3.615A  pdb=" N   ALA R  92 " --> pdb=" O   PRO R  88 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   HIS R  93 " --> pdb=" O   PHE R  89 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 88 through 93'
    Processing helix  chain 'R' and resid 105 through 116
      removed outlier: 3.634A  pdb=" N   THR R 110 " --> pdb=" O   CYS R 106 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   SER R 111 " --> pdb=" O   GLU R 107 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LEU R 115 " --> pdb=" O   SER R 111 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 121 through 136
      removed outlier: 3.523A  pdb=" N   ALA R 128 " --> pdb=" O   LEU R 124 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA R 134 " --> pdb=" O   ASP R 130 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 154 through 159
    Processing helix  chain 'R' and resid 159 through 164
    Processing helix  chain 'R' and resid 198 through 203
    Processing helix  chain 'R' and resid 213 through 218
    Processing helix  chain 'R' and resid 219 through 221
      No H-bonds generated for 'chain 'R' and resid 219 through 221'
    Processing helix  chain 'R' and resid 222 through 227
    Processing helix  chain 'R' and resid 228 through 237
      removed outlier: 4.395A  pdb=" N   ASP R 234 " --> pdb=" O   LEU R 230 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   LYS R 235 " --> pdb=" O   GLN R 231 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   SER R 236 " --> pdb=" O   LYS R 232 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 281 through 286
      removed outlier: 3.785A  pdb=" N   ALA R 285 " --> pdb=" O   THR R 281 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TRP R 286 " --> pdb=" O   PHE R 282 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 281 through 286'
    Processing helix  chain 'R' and resid 287 through 291
    Processing helix  chain 'R' and resid 294 through 299
      removed outlier: 3.504A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 312 through 316
    Processing helix  chain 'R' and resid 317 through 326
      removed outlier: 3.762A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ASN R 322 " --> pdb=" O   ASN R 318 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
      removed outlier: 3.623A  pdb=" N   TYR R 326 " --> pdb=" O   ASN R 322 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 317 through 326'
    Processing helix  chain 'R' and resid 329 through 336
      removed outlier: 3.663A  pdb=" N   ARG R 333 " --> pdb=" O   SER R 329 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ILE R 334 " --> pdb=" O   PRO R 330 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA R 335 " --> pdb=" O   ASP R 331 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213
      removed outlier: 3.711A  pdb=" N   LEU A  45 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 9.882A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.888A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 6.509A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.483A  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 62
      removed outlier: 3.550A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 3.759A  pdb=" N   CYS B 121 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 153
      removed outlier: 6.870A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 166
      removed outlier: 3.519A  pdb=" N   CYS B 166 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 190
      removed outlier: 4.826A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 232
      removed outlier: 3.720A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU B 252 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.619A  pdb=" N   SER B 277 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 17 through 21
    Processing sheet with id=AB2, first strand: chain 'N' and resid 36 through 39

    164 hydrogen bonds defined for protein.
    426 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: 0.93

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2272
        1.34 -     1.46: 1719
        1.46 -     1.58: 3153
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 7202
  Sorted by residual:
  bond pdb=" C   VAL R 210 "
       pdb=" N   PRO R 211 "
    ideal  model  delta    sigma   weight residual
    1.334  1.380 -0.046 2.34e-02 1.83e+03 3.89e+00
  bond pdb=" C   LEU R 167 "
       pdb=" N   PRO R 168 "
    ideal  model  delta    sigma   weight residual
    1.334  1.378 -0.044 2.34e-02 1.83e+03 3.53e+00
  bond pdb=" CB  TRP B  99 "
       pdb=" CG  TRP B  99 "
    ideal  model  delta    sigma   weight residual
    1.498  1.445  0.053 3.10e-02 1.04e+03 2.97e+00
  bond pdb=" N   THR R 189 "
       pdb=" CA  THR R 189 "
    ideal  model  delta    sigma   weight residual
    1.462  1.485 -0.023 1.54e-02 4.22e+03 2.23e+00
  bond pdb=" N   PHE B 292 "
       pdb=" CA  PHE B 292 "
    ideal  model  delta    sigma   weight residual
    1.458  1.476 -0.017 1.35e-02 5.49e+03 1.66e+00
  ... (remaining 7197 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 9490
        1.94 -     3.88: 277
        3.88 -     5.81: 55
        5.81 -     7.75: 11
        7.75 -     9.69: 8
  Bond angle restraints: 9841
  Sorted by residual:
  angle pdb=" N   VAL R 152 "
        pdb=" CA  VAL R 152 "
        pdb=" C   VAL R 152 "
      ideal   model   delta    sigma   weight residual
     111.81  107.54    4.27 8.60e-01 1.35e+00 2.47e+01
  angle pdb=" C   SER N 112 "
        pdb=" N   THR N 113 "
        pdb=" CA  THR N 113 "
      ideal   model   delta    sigma   weight residual
     121.54  130.35   -8.81 1.91e+00 2.74e-01 2.13e+01
  angle pdb=" N   VAL R  31 "
        pdb=" CA  VAL R  31 "
        pdb=" C   VAL R  31 "
      ideal   model   delta    sigma   weight residual
     113.42  108.46    4.96 1.17e+00 7.31e-01 1.80e+01
  angle pdb=" C   ARG R 304 "
        pdb=" N   LYS R 305 "
        pdb=" CA  LYS R 305 "
      ideal   model   delta    sigma   weight residual
     121.54  128.97   -7.43 1.91e+00 2.74e-01 1.51e+01
  angle pdb=" C   ASP B 291 "
        pdb=" N   PHE B 292 "
        pdb=" CA  PHE B 292 "
      ideal   model   delta    sigma   weight residual
     123.47  129.23   -5.76 1.53e+00 4.27e-01 1.42e+01
  ... (remaining 9836 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 3746
       17.38 -    34.76: 340
       34.76 -    52.14: 70
       52.14 -    69.51: 8
       69.51 -    86.89: 4
  Dihedral angle restraints: 4168
    sinusoidal: 1330
      harmonic: 2838
  Sorted by residual:
  dihedral pdb=" CB  CYS R 184 "
           pdb=" SG  CYS R 184 "
           pdb=" SG  CYS R 190 "
           pdb=" CB  CYS R 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -11.85  -74.15     1      1.00e+01 1.00e-02 6.98e+01
  dihedral pdb=" CA  ASN R  51 "
           pdb=" C   ASN R  51 "
           pdb=" N   VAL R  52 "
           pdb=" CA  VAL R  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.59   20.41     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  SER R 137 "
           pdb=" C   SER R 137 "
           pdb=" N   PRO R 138 "
           pdb=" CA  PRO R 138 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.14  -19.86     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 4165 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 977
       0.064 -    0.128: 175
       0.128 -    0.191: 26
       0.191 -    0.255: 1
       0.255 -    0.319: 1
  Chirality restraints: 1180
  Sorted by residual:
  chirality pdb=" CB  ILE R 303 "
            pdb=" CA  ILE R 303 "
            pdb=" CG1 ILE R 303 "
            pdb=" CG2 ILE R 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.32 2.00e-01 2.50e+01 2.54e+00
  chirality pdb=" CB  ILE R 153 "
            pdb=" CA  ILE R 153 "
            pdb=" CG1 ILE R 153 "
            pdb=" CG2 ILE R 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.86   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CB  VAL A 248 "
            pdb=" CA  VAL A 248 "
            pdb=" CG1 VAL A 248 "
            pdb=" CG2 VAL A 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.28e-01
  ... (remaining 1177 not shown)

  Planarity restraints: 1240
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 322 "   -0.049 5.00e-02 4.00e+02   7.25e-02 8.40e+00
        pdb=" N   PRO R 323 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO R 323 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO R 323 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.047 5.00e-02 4.00e+02   7.14e-02 8.16e+00
        pdb=" N   PRO B 236 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 210 "   -0.043 5.00e-02 4.00e+02   6.53e-02 6.82e+00
        pdb=" N   PRO R 211 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO R 211 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO R 211 "   -0.037 5.00e-02 4.00e+02
  ... (remaining 1237 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 2471
        2.84 -     3.36: 5803
        3.36 -     3.87: 10703
        3.87 -     4.39: 11913
        4.39 -     4.90: 21258
  Nonbonded interactions: 52148
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   SER B  84 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" OD2 ASP B 247 "
            pdb=" OG1 THR B 249 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" OG  SER R 207 "
            pdb=" OAC 5FW R 601 "
     model   vdw
     2.349 3.040
  nonbonded pdb=" O   PHE R 133 "
            pdb=" OG  SER R 137 "
     model   vdw
     2.352 3.040
  ... (remaining 52143 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.460
  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:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.310
  Find NCS groups from input model:        0.040
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   7204  Z= 0.187
  Angle     :  0.858   9.691   9845  Z= 0.470
  Chirality :  0.052   0.319   1180
  Planarity :  0.006   0.072   1240
  Dihedral  : 14.285  86.892   2318
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  9.06 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  9.71 %
    Favored  : 89.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -6.33 (0.18), residues: 949
  helix: -5.10 (0.08), residues: 306
  sheet: -3.66 (0.31), residues: 191
  loop : -3.70 (0.22), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG N  98 
 TYR   0.017   0.001   TYR B  59 
 PHE   0.013   0.002   PHE N  27 
 TRP   0.015   0.002   TRP A 234 
 HIS   0.008   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 7202)
  covalent geometry    : angle       0.85808 ( 9841)
  SS BOND              : bond        0.00650 (    2)
  SS BOND              : angle       1.34842 (    4)
  hydrogen bonds       : bond        0.32211 (  164)
  hydrogen bonds       : angle      12.49000 (  426)

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 139
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LYS cc_start: 0.7889 (tttt) cc_final: 0.7687 (tttt)
REVERT: A  343 ASP cc_start: 0.8084 (t70) cc_final: 0.7840 (t70)
REVERT: B   99 TRP cc_start: 0.7046 (m-90) cc_final: 0.6773 (m-90)
REVERT: R  279 MET cc_start: 0.8099 (tpt) cc_final: 0.7884 (tpt)
  outliers start: 2
  outliers final: 0
  residues processed: 141
  average time/residue: 0.0985
  time to fit residues: 17.8114
Evaluate side-chains
  112 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 GLN
B 183 HIS
B 225 HIS
B 239 ASN
B 266 HIS
B 295 ASN
G  24 ASN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 123 GLN
** R 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.159232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.130384 restraints weight = 7956.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.129414 restraints weight = 9912.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.130575 restraints weight = 9758.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.130769 restraints weight = 7925.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.131141 restraints weight = 6973.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7204  Z= 0.168
  Angle     :  0.610   5.709   9845  Z= 0.330
  Chirality :  0.044   0.133   1180
  Planarity :  0.005   0.061   1240
  Dihedral  :  6.120  51.448   1034
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.72 %
    Favored  : 81.97 %
  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: -5.73 (0.20), residues: 949
  helix: -4.27 (0.16), residues: 321
  sheet: -3.62 (0.30), residues: 183
  loop : -3.41 (0.24), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 137 
 TYR   0.019   0.001   TYR B  59 
 PHE   0.013   0.002   PHE N 108 
 TRP   0.025   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 7202)
  covalent geometry    : angle       0.60952 ( 9841)
  SS BOND              : bond        0.00423 (    2)
  SS BOND              : angle       0.87216 (    4)
  hydrogen bonds       : bond        0.03975 (  164)
  hydrogen bonds       : angle       7.53888 (  426)

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  343 ASP cc_start: 0.8284 (t70) cc_final: 0.8038 (t70)
REVERT: B  117 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8075 (tt)
REVERT: R  279 MET cc_start: 0.8072 (tpt) cc_final: 0.7485 (ttp)
  outliers start: 15
  outliers final: 9
  residues processed: 129
  average time/residue: 0.0780
  time to fit residues: 13.5931
Evaluate side-chains
  120 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue  216 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 90 optimal weight:    0.6980
   chunk 71 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 24 optimal weight:    0.2980
   chunk 26 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 48 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A 267 GLN
A 271 ASN
A 390 GLN
B 183 HIS
G  24 ASN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.163131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.133394 restraints weight = 7732.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.133763 restraints weight = 8603.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.135107 restraints weight = 7333.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.135263 restraints weight = 5445.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.135509 restraints weight = 5296.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7204  Z= 0.095
  Angle     :  0.520   5.582   9845  Z= 0.281
  Chirality :  0.042   0.139   1180
  Planarity :  0.004   0.057   1240
  Dihedral  :  5.366  59.108   1034
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.33 %
    Favored  : 80.59 %
  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: -5.10 (0.22), residues: 949
  helix: -3.60 (0.21), residues: 324
  sheet: -3.36 (0.31), residues: 181
  loop : -3.12 (0.25), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  52 
 TYR   0.014   0.001   TYR A 360 
 PHE   0.009   0.001   PHE N  29 
 TRP   0.030   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 7202)
  covalent geometry    : angle       0.52024 ( 9841)
  SS BOND              : bond        0.00281 (    2)
  SS BOND              : angle       0.48418 (    4)
  hydrogen bonds       : bond        0.02888 (  164)
  hydrogen bonds       : angle       6.45655 (  426)

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.7561 (mttt) cc_final: 0.7356 (mppt)
REVERT: B  183 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7794 (t70)
REVERT: R   38 ILE cc_start: 0.8496 (mt) cc_final: 0.8265 (mt)
REVERT: R   43 ILE cc_start: 0.8454 (mm) cc_final: 0.8187 (mp)
  outliers start: 20
  outliers final: 10
  residues processed: 128
  average time/residue: 0.0789
  time to fit residues: 13.6585
Evaluate side-chains
  115 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 91 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   chunk 23 optimal weight:    4.9990
   chunk 42 optimal weight:    8.9990
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
B 183 HIS
G  24 ASN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.155874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.128396 restraints weight = 8090.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.126999 restraints weight = 10421.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.128103 restraints weight = 10558.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.128433 restraints weight = 8338.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.128615 restraints weight = 7569.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   7204  Z= 0.224
  Angle     :  0.630   7.527   9845  Z= 0.339
  Chirality :  0.045   0.140   1180
  Planarity :  0.004   0.055   1240
  Dihedral  :  5.979  56.339   1034
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.33 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 18.49 %
    Favored  : 77.50 %
  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: -4.94 (0.23), residues: 949
  helix: -3.44 (0.22), residues: 318
  sheet: -3.29 (0.32), residues: 178
  loop : -3.07 (0.26), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  42 
 TYR   0.013   0.002   TYR N  32 
 PHE   0.018   0.002   PHE N 108 
 TRP   0.017   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 ( 7202)
  covalent geometry    : angle       0.62951 ( 9841)
  SS BOND              : bond        0.00356 (    2)
  SS BOND              : angle       0.67435 (    4)
  hydrogen bonds       : bond        0.03476 (  164)
  hydrogen bonds       : angle       6.41138 (  426)

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   24 LYS cc_start: 0.7720 (mttt) cc_final: 0.7439 (mppt)
REVERT: A  343 ASP cc_start: 0.8351 (t70) cc_final: 0.8110 (t70)
REVERT: B   45 MET cc_start: 0.8329 (mtm) cc_final: 0.8024 (mtm)
  outliers start: 26
  outliers final: 18
  residues processed: 143
  average time/residue: 0.0801
  time to fit residues: 15.5707
Evaluate side-chains
  135 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  184 CYS
Chi-restraints excluded: chain R residue  216 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 91 optimal weight:    0.3980
   chunk 31 optimal weight:    7.9990
   chunk 52 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
G  24 ASN
** N  82 GLN ** 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 = 0.3784 r_free = 0.3784 target = 0.157809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.129009 restraints weight = 7989.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.127896 restraints weight = 10296.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.129191 restraints weight = 9780.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.129372 restraints weight = 7315.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.129647 restraints weight = 6675.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7204  Z= 0.157
  Angle     :  0.578   5.990   9845  Z= 0.312
  Chirality :  0.044   0.132   1180
  Planarity :  0.004   0.055   1240
  Dihedral  :  5.729  55.156   1034
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 19.41 %
    Favored  : 76.43 %
  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: -4.72 (0.24), residues: 949
  helix: -3.24 (0.23), residues: 318
  sheet: -3.30 (0.32), residues: 177
  loop : -2.88 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 239 
 TYR   0.011   0.001   TYR A 360 
 PHE   0.012   0.001   PHE A 238 
 TRP   0.041   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 7202)
  covalent geometry    : angle       0.57846 ( 9841)
  SS BOND              : bond        0.00346 (    2)
  SS BOND              : angle       0.59331 (    4)
  hydrogen bonds       : bond        0.03095 (  164)
  hydrogen bonds       : angle       6.21576 (  426)

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   24 LYS cc_start: 0.7621 (mttt) cc_final: 0.7377 (mppt)
REVERT: A  270 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8092 (tt)
REVERT: B   45 MET cc_start: 0.8305 (mtm) cc_final: 0.8019 (mtm)
REVERT: R   38 ILE cc_start: 0.8558 (mt) cc_final: 0.8342 (mt)
REVERT: R   82 MET cc_start: 0.7903 (mtp) cc_final: 0.7686 (mtp)
  outliers start: 27
  outliers final: 19
  residues processed: 136
  average time/residue: 0.0779
  time to fit residues: 14.4316
Evaluate side-chains
  133 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  184 CYS
Chi-restraints excluded: chain R residue  216 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   chunk 93 optimal weight:    0.0980
   chunk 24 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 58 optimal weight:    7.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
G  24 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.160420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.132091 restraints weight = 7938.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.130727 restraints weight = 10306.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.132395 restraints weight = 9672.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.132648 restraints weight = 7084.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.132990 restraints weight = 6397.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7204  Z= 0.116
  Angle     :  0.549   9.327   9845  Z= 0.292
  Chirality :  0.042   0.135   1180
  Planarity :  0.004   0.053   1240
  Dihedral  :  5.308  55.828   1034
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 20.18 %
    Favored  : 75.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.51 (0.24), residues: 949
  helix: -3.01 (0.24), residues: 323
  sheet: -3.20 (0.32), residues: 179
  loop : -2.77 (0.27), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 239 
 TYR   0.012   0.001   TYR A 360 
 PHE   0.009   0.001   PHE A 340 
 TRP   0.057   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7202)
  covalent geometry    : angle       0.54936 ( 9841)
  SS BOND              : bond        0.00278 (    2)
  SS BOND              : angle       0.42369 (    4)
  hydrogen bonds       : bond        0.02769 (  164)
  hydrogen bonds       : angle       5.87808 (  426)

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 110
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A   24 LYS cc_start: 0.7509 (mttt) cc_final: 0.7282 (mppt)
REVERT: A  270 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8133 (tt)
REVERT: A  291 LEU cc_start: 0.7335 (mt) cc_final: 0.7097 (mt)
REVERT: B   45 MET cc_start: 0.8286 (mtm) cc_final: 0.8027 (mtm)
REVERT: R   38 ILE cc_start: 0.8515 (mt) cc_final: 0.8302 (mt)
  outliers start: 31
  outliers final: 25
  residues processed: 132
  average time/residue: 0.0817
  time to fit residues: 14.6181
Evaluate side-chains
  129 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  184 CYS
Chi-restraints excluded: chain R residue  216 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 31 optimal weight:   10.0000
   chunk 28 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0670
   chunk 8 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 75 optimal weight:    0.0170
   chunk 17 optimal weight:    6.9990
   chunk 9 optimal weight:    0.7980
   chunk 73 optimal weight:   10.0000
   chunk 63 optimal weight:    0.0980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
G  24 ASN
N  53 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.164044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.134237 restraints weight = 7877.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.134260 restraints weight = 9670.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.135642 restraints weight = 7121.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.135576 restraints weight = 5539.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.135801 restraints weight = 5144.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.2480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7204  Z= 0.099
  Angle     :  0.531   8.686   9845  Z= 0.281
  Chirality :  0.042   0.138   1180
  Planarity :  0.003   0.051   1240
  Dihedral  :  5.058  56.627   1034
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 20.65 %
    Favored  : 75.81 %
  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: -4.29 (0.25), residues: 949
  helix: -2.77 (0.25), residues: 319
  sheet: -3.25 (0.32), residues: 181
  loop : -2.61 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 239 
 TYR   0.012   0.001   TYR A 360 
 PHE   0.008   0.001   PHE A 340 
 TRP   0.064   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 7202)
  covalent geometry    : angle       0.53078 ( 9841)
  SS BOND              : bond        0.00247 (    2)
  SS BOND              : angle       0.34180 (    4)
  hydrogen bonds       : bond        0.02618 (  164)
  hydrogen bonds       : angle       5.68546 (  426)

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A   24 LYS cc_start: 0.7387 (mttt) cc_final: 0.7168 (mppt)
REVERT: A  270 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8190 (tt)
REVERT: B   45 MET cc_start: 0.8277 (mtm) cc_final: 0.8066 (mtm)
REVERT: R   38 ILE cc_start: 0.8558 (mt) cc_final: 0.8292 (mt)
  outliers start: 23
  outliers final: 20
  residues processed: 125
  average time/residue: 0.0790
  time to fit residues: 13.4020
Evaluate side-chains
  123 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain R residue  184 CYS
Chi-restraints excluded: chain R residue  216 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 83 optimal weight:    0.4980
   chunk 42 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 93 optimal weight:    7.9990
   chunk 44 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   overall best weight:    2.2988

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

Flipped N/Q/H residues before XYZ refinement:
B 183 HIS
B 340 ASN
G  24 ASN
N  53 GLN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.155729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.128124 restraints weight = 8124.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.126656 restraints weight = 10932.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.127940 restraints weight = 11167.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.127972 restraints weight = 8312.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.128510 restraints weight = 7349.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   7204  Z= 0.204
  Angle     :  0.623   7.148   9845  Z= 0.331
  Chirality :  0.045   0.134   1180
  Planarity :  0.004   0.050   1240
  Dihedral  :  5.737  54.575   1034
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.12 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 21.73 %
    Favored  : 74.11 %
  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: -4.37 (0.25), residues: 949
  helix: -2.82 (0.25), residues: 318
  sheet: -3.47 (0.30), residues: 196
  loop : -2.53 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 239 
 TYR   0.012   0.001   TYR N  32 
 PHE   0.017   0.002   PHE A 212 
 TRP   0.066   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 7202)
  covalent geometry    : angle       0.62309 ( 9841)
  SS BOND              : bond        0.00333 (    2)
  SS BOND              : angle       0.63188 (    4)
  hydrogen bonds       : bond        0.03355 (  164)
  hydrogen bonds       : angle       5.96384 (  426)

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A   24 LYS cc_start: 0.7616 (mttt) cc_final: 0.7339 (mppt)
REVERT: A  270 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8127 (tt)
REVERT: A  343 ASP cc_start: 0.8268 (t70) cc_final: 0.8024 (t70)
REVERT: B   45 MET cc_start: 0.8289 (mtm) cc_final: 0.8041 (mtm)
  outliers start: 27
  outliers final: 23
  residues processed: 123
  average time/residue: 0.0807
  time to fit residues: 13.5646
Evaluate side-chains
  124 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  184 CYS
Chi-restraints excluded: chain R residue  216 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9990
   chunk 36 optimal weight:    0.4980
   chunk 27 optimal weight:    0.4980
   chunk 35 optimal weight:    0.0870
   chunk 8 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.5760

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

Flipped N/Q/H residues before XYZ refinement:
A 227 GLN
B 340 ASN
G  24 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.161977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.132337 restraints weight = 7791.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.132996 restraints weight = 6982.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.133846 restraints weight = 6246.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.134635 restraints weight = 5626.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.135078 restraints weight = 5166.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.2666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7204  Z= 0.098
  Angle     :  0.540   7.677   9845  Z= 0.286
  Chirality :  0.042   0.140   1180
  Planarity :  0.003   0.052   1240
  Dihedral  :  5.114  55.823   1034
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 22.80 %
    Favored  : 73.50 %
  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: -4.09 (0.25), residues: 949
  helix: -2.50 (0.26), residues: 323
  sheet: -3.14 (0.32), residues: 177
  loop : -2.59 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 239 
 TYR   0.013   0.001   TYR A 360 
 PHE   0.020   0.001   PHE A 212 
 TRP   0.044   0.002   TRP B  82 
 HIS   0.002   0.000   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 7202)
  covalent geometry    : angle       0.53999 ( 9841)
  SS BOND              : bond        0.00240 (    2)
  SS BOND              : angle       0.37483 (    4)
  hydrogen bonds       : bond        0.02632 (  164)
  hydrogen bonds       : angle       5.61690 (  426)

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A   24 LYS cc_start: 0.7401 (mttt) cc_final: 0.7154 (mppt)
REVERT: A  270 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8133 (tt)
  outliers start: 24
  outliers final: 15
  residues processed: 123
  average time/residue: 0.0784
  time to fit residues: 13.1754
Evaluate side-chains
  117 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain R residue  184 CYS
Chi-restraints excluded: chain R residue  216 VAL
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  303 ILE
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0050
   chunk 66 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 28 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9990
   chunk 5 optimal weight:    8.9990
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
G  24 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.162505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.133072 restraints weight = 7783.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.133422 restraints weight = 8949.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.134193 restraints weight = 7286.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.134189 restraints weight = 5835.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.134687 restraints weight = 5553.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7204  Z= 0.101
  Angle     :  0.532   7.332   9845  Z= 0.280
  Chirality :  0.042   0.135   1180
  Planarity :  0.003   0.048   1240
  Dihedral  :  4.930  57.431   1034
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 23.57 %
    Favored  : 73.81 %
  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: -3.85 (0.25), residues: 949
  helix: -2.31 (0.27), residues: 319
  sheet: -2.95 (0.32), residues: 179
  loop : -2.47 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 239 
 TYR   0.014   0.001   TYR A 360 
 PHE   0.020   0.001   PHE A 212 
 TRP   0.037   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 7202)
  covalent geometry    : angle       0.53192 ( 9841)
  SS BOND              : bond        0.00223 (    2)
  SS BOND              : angle       0.32340 (    4)
  hydrogen bonds       : bond        0.02610 (  164)
  hydrogen bonds       : angle       5.39708 (  426)

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

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

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1898 Ramachandran restraints generated.
    949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A   24 LYS cc_start: 0.7314 (mttt) cc_final: 0.7040 (mppt)
REVERT: A  270 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7940 (tt)
  outliers start: 17
  outliers final: 14
  residues processed: 115
  average time/residue: 0.0682
  time to fit residues: 11.0194
Evaluate side-chains
  114 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue  184 CYS
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  275 LEU
Chi-restraints excluded: chain R residue  303 ILE
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 61 optimal weight:    5.9990
   chunk 31 optimal weight:    0.0470
   chunk 57 optimal weight:    0.7980
   chunk 91 optimal weight:    0.4980
   chunk 25 optimal weight:    3.9990
   chunk 81 optimal weight:    9.9990
   chunk 5 optimal weight:    7.9990
   chunk 90 optimal weight:    7.9990
   chunk 87 optimal weight:    0.4980
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
A 227 GLN
B 340 ASN
G  24 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.165349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.138762 restraints weight = 7615.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.138003 restraints weight = 8993.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.138774 restraints weight = 8577.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.139024 restraints weight = 7542.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.139278 restraints weight = 6451.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7204  Z= 0.093
  Angle     :  0.523   7.283   9845  Z= 0.275
  Chirality :  0.042   0.136   1180
  Planarity :  0.003   0.047   1240
  Dihedral  :  4.744  58.752   1034
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 24.50 %
    Favored  : 72.73 %
  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: -3.72 (0.25), residues: 949
  helix: -2.23 (0.27), residues: 326
  sheet: -2.76 (0.33), residues: 182
  loop : -2.41 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 239 
 TYR   0.014   0.001   TYR A 360 
 PHE   0.020   0.001   PHE A 212 
 TRP   0.033   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 7202)
  covalent geometry    : angle       0.52330 ( 9841)
  SS BOND              : bond        0.00205 (    2)
  SS BOND              : angle       0.26879 (    4)
  hydrogen bonds       : bond        0.02484 (  164)
  hydrogen bonds       : angle       5.26495 (  426)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1155.37 seconds
wall clock time: 20 minutes 34.11 seconds (1234.11 seconds total)