Starting phenix.real_space_refine
on Fri Jul 25 02:24:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dhr_30682/07_2025/7dhr_30682.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dhr_30682/07_2025/7dhr_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_30682/07_2025/7dhr_30682.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dhr_30682/07_2025/7dhr_30682.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dhr_30682/07_2025/7dhr_30682.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dhr_30682/07_2025/7dhr_30682.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 8}
          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: {'GLN:plan1': 6, 'GLU:plan': 6, 'ARG:plan': 14, 'ASN:plan1': 4, 'ASP:plan': 13}
          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: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          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: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 5}
          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: 5.33, per 1000 atoms: 0.76
  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: 1.78
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  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: 0.92
  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: 1.92

  Time building geometry restraints manager: 1.99 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:             125.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     20.830
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  151.840
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.015   0.002   TRP A 234 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.013   0.002   PHE N  27 
 TYR   0.017   0.001   TYR B  59 
 ARG   0.005   0.001   ARG N  98 

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

*********************** 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  : 0.705 
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: 0.2646
  time to fit residues: 47.9181
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  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 80 optimal weight:    0.2980
   chunk 72 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 74 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0010
   chunk 45 optimal weight:    0.9980
   chunk 55 optimal weight:    0.3980
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.4586

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A 278 ASN
A 384 GLN
A 390 GLN
B 183 HIS
B 225 HIS
B 239 ASN
B 266 HIS
B 295 ASN
G  24 ASN
R  65 GLN
R 229 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.168681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.141659 restraints weight = 7646.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.139722 restraints weight = 9415.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.140587 restraints weight = 9110.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.1562

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= 0.091
  Angle     :  0.537   5.487   9845  Z= 0.291
  Chirality :  0.042   0.140   1180
  Planarity :  0.004   0.058   1240
  Dihedral  :  5.527  59.093   1034
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 14.64 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.64 (0.20), residues: 949
  helix: -4.22 (0.16), residues: 321
  sheet: -3.56 (0.29), residues: 188
  loop : -3.32 (0.24), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R  93 
 PHE   0.013   0.001   PHE N  29 
 TYR   0.011   0.001   TYR B  59 
 ARG   0.005   0.000   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03168 (  164)
  hydrogen bonds       : angle       7.30643 (  426)
  SS BOND              : bond        0.00344 (    2)
  SS BOND              : angle       1.00401 (    4)
  covalent geometry    : bond        0.00195 ( 7202)
  covalent geometry    : angle       0.53649 ( 9841)

*********************** 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: 16
    poor density    : 119
  time to evaluate  : 0.744 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.7656 (mttt) cc_final: 0.7450 (mppt)
REVERT: A  283 ARG cc_start: 0.7352 (ttp-110) cc_final: 0.7096 (ttp-110)
REVERT: B   61 MET cc_start: 0.8892 (ppp) cc_final: 0.8683 (ppp)
REVERT: R   36 MET cc_start: 0.7004 (tpp) cc_final: 0.6788 (tpp)
REVERT: R   38 ILE cc_start: 0.8444 (mt) cc_final: 0.8204 (mt)
  outliers start: 16
  outliers final: 8
  residues processed: 129
  average time/residue: 0.1882
  time to fit residues: 32.5514
Evaluate side-chains
  111 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
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  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 65 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 40 optimal weight:    6.9990
   chunk 62 optimal weight:    0.7980
   chunk 68 optimal weight:    0.2980
   chunk 28 optimal weight:    0.5980
   chunk 78 optimal weight:    0.0060
   chunk 60 optimal weight:    0.3980
   chunk 20 optimal weight:    9.9990
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
A 384 GLN
A 390 GLN
G  24 ASN
R 229 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.170315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.144791 restraints weight = 7737.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.141905 restraints weight = 8325.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.143775 restraints weight = 8721.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.1942

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= 0.084
  Angle     :  0.495   5.521   9845  Z= 0.268
  Chirality :  0.041   0.135   1180
  Planarity :  0.004   0.053   1240
  Dihedral  :  5.009  56.223   1034
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.64 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.99 (0.22), residues: 949
  helix: -3.58 (0.21), residues: 326
  sheet: -3.27 (0.30), residues: 189
  loop : -2.97 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 234 
 HIS   0.003   0.000   HIS A 357 
 PHE   0.026   0.001   PHE A 212 
 TYR   0.011   0.001   TYR B 289 
 ARG   0.002   0.000   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02789 (  164)
  hydrogen bonds       : angle       6.26398 (  426)
  SS BOND              : bond        0.00257 (    2)
  SS BOND              : angle       0.48639 (    4)
  covalent geometry    : bond        0.00182 ( 7202)
  covalent geometry    : angle       0.49493 ( 9841)

*********************** 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
  127 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.758 
Fit side-chains
REVERT: A   24 LYS cc_start: 0.7424 (mttt) cc_final: 0.7201 (mppt)
REVERT: A  291 LEU cc_start: 0.7333 (mt) cc_final: 0.7080 (mt)
REVERT: B  101 MET cc_start: 0.8363 (mtt) cc_final: 0.8139 (mtt)
REVERT: B  258 ASP cc_start: 0.7620 (m-30) cc_final: 0.6589 (t0)
REVERT: N   60 TYR cc_start: 0.8531 (m-80) cc_final: 0.7921 (m-80)
REVERT: R   36 MET cc_start: 0.7012 (tpp) cc_final: 0.6786 (tpp)
REVERT: R   38 ILE cc_start: 0.8489 (mt) cc_final: 0.8225 (mt)
REVERT: R  156 MET cc_start: 0.6560 (ttm) cc_final: 0.6109 (tmm)
  outliers start: 15
  outliers final: 7
  residues processed: 122
  average time/residue: 0.2009
  time to fit residues: 33.0507
Evaluate side-chains
  109 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
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  147 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain R residue   43 ILE
Chi-restraints excluded: chain R residue  216 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 58 optimal weight:    5.9990
   chunk 13 optimal weight:   40.0000
   chunk 83 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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**
N 123 GLN
R  65 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.153967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.126130 restraints weight = 8224.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.124636 restraints weight = 11292.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.125780 restraints weight = 11479.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055   7204  Z= 0.286
  Angle     :  0.687   7.447   9845  Z= 0.370
  Chirality :  0.048   0.187   1180
  Planarity :  0.005   0.057   1240
  Dihedral  :  6.315  59.448   1034
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.85 %
    Favored  : 89.15 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 19.26 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.95 (0.23), residues: 949
  helix: -3.53 (0.22), residues: 317
  sheet: -3.32 (0.32), residues: 177
  loop : -3.00 (0.26), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP B  82 
 HIS   0.008   0.002   HIS A 357 
 PHE   0.024   0.002   PHE N 108 
 TYR   0.019   0.002   TYR N  32 
 ARG   0.004   0.001   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03943 (  164)
  hydrogen bonds       : angle       6.55453 (  426)
  SS BOND              : bond        0.00389 (    2)
  SS BOND              : angle       0.85160 (    4)
  covalent geometry    : bond        0.00673 ( 7202)
  covalent geometry    : angle       0.68708 ( 9841)

*********************** 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
  143 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 MET cc_start: 0.8337 (mtm) cc_final: 0.8056 (mtm)
REVERT: R   36 MET cc_start: 0.6986 (tpp) cc_final: 0.6752 (tpp)
REVERT: R  170 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7518 (mm-40)
  outliers start: 22
  outliers final: 15
  residues processed: 136
  average time/residue: 0.2980
  time to fit residues: 54.5862
Evaluate side-chains
  131 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
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  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 N residue   51 ILE
Chi-restraints excluded: chain N residue   79 LEU
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 40 optimal weight:    3.9990
   chunk 64 optimal weight:    0.0670
   chunk 42 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 56 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.7122

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
A 271 ASN
A 362 HIS
B 340 ASN
G  24 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.161885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.132332 restraints weight = 7677.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.133332 restraints weight = 8050.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.135021 restraints weight = 6615.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7204  Z= 0.099
  Angle     :  0.522   5.629   9845  Z= 0.283
  Chirality :  0.042   0.139   1180
  Planarity :  0.004   0.055   1240
  Dihedral  :  5.381  59.801   1034
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 22.19 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.59 (0.24), residues: 949
  helix: -3.10 (0.24), residues: 321
  sheet: -3.23 (0.33), residues: 176
  loop : -2.84 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.020   0.001   PHE A 212 
 TYR   0.015   0.001   TYR A 360 
 ARG   0.004   0.000   ARG R 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02730 (  164)
  hydrogen bonds       : angle       5.94110 (  426)
  SS BOND              : bond        0.00294 (    2)
  SS BOND              : angle       0.46790 (    4)
  covalent geometry    : bond        0.00222 ( 7202)
  covalent geometry    : angle       0.52191 ( 9841)

*********************** 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
  138 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 1.101 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.7548 (mttt) cc_final: 0.7342 (mppt)
REVERT: A  270 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8172 (tt)
REVERT: B   45 MET cc_start: 0.8246 (mtm) cc_final: 0.7982 (mtm)
REVERT: N   83 MET cc_start: 0.5882 (tpt) cc_final: 0.5663 (tpt)
REVERT: R   38 ILE cc_start: 0.8558 (mt) cc_final: 0.8338 (mt)
  outliers start: 21
  outliers final: 16
  residues processed: 131
  average time/residue: 0.2722
  time to fit residues: 49.1044
Evaluate side-chains
  124 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 1.992 
-------------------------------------------------------------------------------
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   93 ILE
Chi-restraints excluded: chain B residue  147 SER
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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 77 optimal weight:    0.4980
   chunk 87 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   overall best weight:    1.0584

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.161097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.131144 restraints weight = 7898.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.131177 restraints weight = 9108.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.132597 restraints weight = 7503.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7204  Z= 0.118
  Angle     :  0.542   9.545   9845  Z= 0.287
  Chirality :  0.042   0.131   1180
  Planarity :  0.004   0.052   1240
  Dihedral  :  5.257  58.822   1034
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 21.88 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.37 (0.24), residues: 949
  helix: -2.85 (0.25), residues: 319
  sheet: -3.19 (0.33), residues: 177
  loop : -2.73 (0.27), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.017   0.001   PHE A 212 
 TYR   0.012   0.001   TYR A 360 
 ARG   0.007   0.000   ARG R 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02713 (  164)
  hydrogen bonds       : angle       5.73379 (  426)
  SS BOND              : bond        0.00271 (    2)
  SS BOND              : angle       0.42023 (    4)
  covalent geometry    : bond        0.00272 ( 7202)
  covalent geometry    : angle       0.54193 ( 9841)

*********************** 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
  129 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.7456 (mttt) cc_final: 0.7252 (mppt)
REVERT: A  270 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8089 (tt)
REVERT: B   45 MET cc_start: 0.8212 (mtm) cc_final: 0.7935 (mtm)
REVERT: R   38 ILE cc_start: 0.8570 (mt) cc_final: 0.8342 (mt)
  outliers start: 21
  outliers final: 14
  residues processed: 124
  average time/residue: 0.2825
  time to fit residues: 50.7649
Evaluate side-chains
  119 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
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   93 ILE
Chi-restraints excluded: chain B residue  147 SER
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 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 56 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 13 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   chunk 90 optimal weight:    0.0980
   chunk 88 optimal weight:    0.0370
   chunk 39 optimal weight:    4.9990
   overall best weight:    0.5258

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.164426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.138301 restraints weight = 7653.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.136139 restraints weight = 8435.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.136945 restraints weight = 8538.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7204  Z= 0.092
  Angle     :  0.516   9.060   9845  Z= 0.274
  Chirality :  0.042   0.138   1180
  Planarity :  0.003   0.053   1240
  Dihedral  :  4.835  56.783   1034
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 23.11 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.14 (0.25), residues: 949
  helix: -2.61 (0.26), residues: 325
  sheet: -3.11 (0.32), residues: 181
  loop : -2.58 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.001   TRP B  82 
 HIS   0.003   0.000   HIS A 357 
 PHE   0.017   0.001   PHE A 212 
 TYR   0.012   0.001   TYR A 360 
 ARG   0.007   0.000   ARG R 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02491 (  164)
  hydrogen bonds       : angle       5.45231 (  426)
  SS BOND              : bond        0.00215 (    2)
  SS BOND              : angle       0.29040 (    4)
  covalent geometry    : bond        0.00203 ( 7202)
  covalent geometry    : angle       0.51578 ( 9841)

*********************** 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
  125 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.7338 (mttt) cc_final: 0.7110 (mppt)
REVERT: A  270 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8099 (tt)
REVERT: B   45 MET cc_start: 0.8195 (mtm) cc_final: 0.7982 (mtm)
REVERT: R   38 ILE cc_start: 0.8448 (mt) cc_final: 0.8170 (mt)
  outliers start: 20
  outliers final: 14
  residues processed: 119
  average time/residue: 0.1893
  time to fit residues: 30.5015
Evaluate side-chains
  115 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  296 VAL
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain G residue   22 GLU
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 73 optimal weight:    6.9990
   chunk 94 optimal weight:    0.0170
   chunk 48 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 61 optimal weight:    8.9990
   chunk 11 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9980
   overall best weight:    1.4022

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

Flipped N/Q/H residues before XYZ refinement:
G  24 ASN
N  53 GLN
** 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 = 0.3791 r_free = 0.3791 target = 0.159702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.131547 restraints weight = 7781.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.130536 restraints weight = 9624.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.131843 restraints weight = 9673.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7204  Z= 0.138
  Angle     :  0.555   8.024   9845  Z= 0.295
  Chirality :  0.043   0.134   1180
  Planarity :  0.004   0.050   1240
  Dihedral  :  5.098  55.634   1034
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 22.65 %
    Favored  : 74.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.09 (0.25), residues: 949
  helix: -2.56 (0.26), residues: 325
  sheet: -3.10 (0.32), residues: 183
  loop : -2.54 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.021   0.001   PHE A 212 
 TYR   0.010   0.001   TYR A 360 
 ARG   0.007   0.001   ARG R 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02804 (  164)
  hydrogen bonds       : angle       5.51800 (  426)
  SS BOND              : bond        0.00253 (    2)
  SS BOND              : angle       0.41919 (    4)
  covalent geometry    : bond        0.00322 ( 7202)
  covalent geometry    : angle       0.55550 ( 9841)

*********************** 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
  127 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.7403 (mttt) cc_final: 0.7149 (mppt)
REVERT: A  270 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8166 (tt)
REVERT: B   45 MET cc_start: 0.8247 (mtm) cc_final: 0.8005 (mtm)
REVERT: R   38 ILE cc_start: 0.8470 (mt) cc_final: 0.8178 (mt)
REVERT: R  279 MET cc_start: 0.6926 (tpt) cc_final: 0.6678 (ttt)
  outliers start: 20
  outliers final: 15
  residues processed: 123
  average time/residue: 0.2589
  time to fit residues: 43.6183
Evaluate side-chains
  120 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 1.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  147 SER
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 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 37 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 8 optimal weight:    0.3980
   chunk 22 optimal weight:    7.9990
   chunk 34 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 61 optimal weight:    9.9990
   chunk 81 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3823 r_free = 0.3823 target = 0.162961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.134167 restraints weight = 7741.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.133233 restraints weight = 9767.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.134766 restraints weight = 9145.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7204  Z= 0.102
  Angle     :  0.532   7.866   9845  Z= 0.280
  Chirality :  0.042   0.132   1180
  Planarity :  0.003   0.050   1240
  Dihedral  :  4.842  54.975   1034
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 23.57 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.89 (0.25), residues: 949
  helix: -2.41 (0.27), residues: 330
  sheet: -2.84 (0.33), residues: 177
  loop : -2.49 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.020   0.001   PHE A 212 
 TYR   0.013   0.001   TYR A 360 
 ARG   0.006   0.000   ARG R 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02530 (  164)
  hydrogen bonds       : angle       5.33247 (  426)
  SS BOND              : bond        0.00225 (    2)
  SS BOND              : angle       0.35887 (    4)
  covalent geometry    : bond        0.00231 ( 7202)
  covalent geometry    : angle       0.53244 ( 9841)

*********************** 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
  126 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 1.116 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.7326 (mttt) cc_final: 0.7039 (mppt)
REVERT: A  270 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8180 (tt)
REVERT: B   45 MET cc_start: 0.8225 (mtm) cc_final: 0.8022 (mtm)
REVERT: R   38 ILE cc_start: 0.8520 (mt) cc_final: 0.8249 (mt)
  outliers start: 19
  outliers final: 16
  residues processed: 120
  average time/residue: 0.3068
  time to fit residues: 51.0065
Evaluate side-chains
  120 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
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   29 THR
Chi-restraints excluded: chain B residue  147 SER
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 87 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0980
   chunk 36 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 68 optimal weight:    3.9990
   chunk 74 optimal weight:    0.0010
   chunk 12 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   overall best weight:    0.3986

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.168588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.136803 restraints weight = 7930.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.139225 restraints weight = 6336.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.140097 restraints weight = 5408.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7204  Z= 0.088
  Angle     :  0.520   8.006   9845  Z= 0.272
  Chirality :  0.042   0.135   1180
  Planarity :  0.003   0.050   1240
  Dihedral  :  4.643  52.203   1034
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 24.19 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.73 (0.25), residues: 949
  helix: -2.31 (0.27), residues: 340
  sheet: -2.59 (0.33), residues: 181
  loop : -2.43 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP B  82 
 HIS   0.002   0.000   HIS A 220 
 PHE   0.021   0.001   PHE A 212 
 TYR   0.013   0.001   TYR A 360 
 ARG   0.006   0.000   ARG R 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02384 (  164)
  hydrogen bonds       : angle       5.18191 (  426)
  SS BOND              : bond        0.00194 (    2)
  SS BOND              : angle       0.27021 (    4)
  covalent geometry    : bond        0.00194 ( 7202)
  covalent geometry    : angle       0.52006 ( 9841)

********************** 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
  115 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.708 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.7311 (mttt) cc_final: 0.6719 (mmtm)
REVERT: A  270 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7997 (tt)
REVERT: N   83 MET cc_start: 0.5780 (tpt) cc_final: 0.5527 (tpt)
REVERT: R   38 ILE cc_start: 0.8634 (mt) cc_final: 0.8404 (mt)
REVERT: R  156 MET cc_start: 0.6649 (ttm) cc_final: 0.6224 (tmm)
  outliers start: 15
  outliers final: 11
  residues processed: 111
  average time/residue: 0.1675
  time to fit residues: 25.8974
Evaluate side-chains
  108 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 1.417 
-------------------------------------------------------------------------------
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   29 THR
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 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  275 LEU
Chi-restraints excluded: chain R residue  303 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 72 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 21 optimal weight:    0.0870
   chunk 92 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 63 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.7760

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.164343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.138172 restraints weight = 7657.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.135936 restraints weight = 9241.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.136979 restraints weight = 9458.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7204  Z= 0.101
  Angle     :  0.523   7.502   9845  Z= 0.274
  Chirality :  0.042   0.133   1180
  Planarity :  0.003   0.049   1240
  Dihedral  :  4.572  48.018   1034
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 24.65 %
    Favored  : 72.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.63 (0.25), residues: 949
  helix: -2.18 (0.28), residues: 327
  sheet: -2.58 (0.33), residues: 183
  loop : -2.39 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.019   0.001   PHE A 212 
 TYR   0.012   0.001   TYR A 360 
 ARG   0.006   0.001   ARG R 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02459 (  164)
  hydrogen bonds       : angle       5.14968 (  426)
  SS BOND              : bond        0.00209 (    2)
  SS BOND              : angle       0.30618 (    4)
  covalent geometry    : bond        0.00229 ( 7202)
  covalent geometry    : angle       0.52270 ( 9841)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3410.22 seconds
wall clock time: 64 minutes 40.01 seconds (3880.01 seconds total)